Pick an example everyone knows: Bach's Prelude in C. I wrote in chord symbols over every bar of that, except for that one very weird bar near the end. It helped me a lot in memorizing it.
By the way, a 19th century functional harmonist would also find that prelude sort of odd. Not in terms of the chords themselves, but they don't always obey their usual functions.
Also, many modern players and theorists reach toward Schenkerian analysis and its derivatives to sort of explain why music sounds the ways it does. Unlike counterpoint and harmony, Schenkerian analysis is almost entirely descriptive, not prescriptive. I have no idea what your teacher would have suggested.
I don't even understand this paragraph. I'm not arguing.
As someone with a significant background in historical performance, my books of Bach preludes are still full of Roman numerals because that is a really good way to "compress" information about what notes to play.
I'm actually interested in other ways of analyzing it.
* Schenkerian analysis is probably the modern method of looking at Bach. A sister comment also indicates that Schenker was a controversial figure (he was a German fascist), but I believe the follow-ups from other theorists on his methods are the modern ones to use for analysis.
* Analyzing otherwise in the context of counterpoint and intervals - see Gradus ad Parnassum and Kennan's book on counterpoint.
It’s also, interestingly, illustrative of your argument. Musical analysis is necessarily socially contextual and therefore revealing of the author’s values and priorities, and Schenkerian arguments often imply, or directly come with, some really quite right-wing positions. Schenker was very much into motivated reasoning to defend his deep-rooted racism; many Schenkerian analysts have, deliberately or otherwise, wound up following in those footsteps.
It's true though that Schenker's treatises included plenty of political asides of such an extreme chauvistic character that to call them "quite right wing" is a huge understatement. (It's also true that, as scholarly research has pointed out in recent years, he seems to have expressed similarly extreme views in his private correspondence and other private writings.) Part of this might perhaps be explained as Schenker's awkward overcompensation for what would've been his remarkably humble origins back then (he came from a small village in what was then Austrian Galicia, now in modern Ukraine). Regardless, I think we nowadays have so many sources proving the relevance of melodic reduction/elaboration approaches (some of them quite early indeed, from the 16th-17th centuries) that to tie these analytical approaches polemically to Schenker and his specificities is really quite pointless, perhaps even misleading.
I'm curious what you would suggest to perform a modern analysis of Bach (what the original comment chain on this was about) if not Schenkerian analysis. I didn't see any alternative analysis tools proposed in your post, even though it sounds like you are educated on the subject.
Andras Schiff playing BWV 903 (there are some REALLY bad performances of this piece out there): https://www.youtube.com/watch?v=SNWOhm5iXxs
BWV 1079 wasn't necessarily written with musical instruments proscribed, but here's a good French group's performance: https://www.youtube.com/watch?v=tfMQ-AYiuJw
My piano teacher pointed me to this recording when I studied the piece with him. It was scandalizing at first, but the free improvisation in the arpeggiated chords is almost miraculous. (I also love Paul Badura-Skoda's take on the piece: https://www.youtube.com/watch?v=Xx5gojkXdeI)
When theorists talk about Scarlatti laying the foundation of harmony, partimento is probably the foundation they are referring to. Functional harmony of the 19th century is just a more powerful abstraction.
Second, while they did think differently about harmony, you can describe it in modern terms. A description like Cmaj7 doesn't mean anything else than a set of pitches.
A tritone substitution is somewhat different, since it depends on what the analyzer thinks the chord could/should have been. There's a recent YouTube video (by David Bennett, IIRC) that shows tritone substitutions in songs, but he mentions that he doubts Paul McCartney knew he was writing one. But does that mean it isn't? No, it means you can see it as a tritone substitution.
Music theory is a subjective tool to describe and compare, nothing else.
I think this might be missing the point a little bit - the bassline in figured bass has more primacy than any of the sonorities above it. The most relevant feature of "chord"-based approaches to music (as found historically, e.g. in performance methods for the Baroque guitar, and to a far lesser extent in repertoire for the lute) is that the vertical sonority (such as "Cmaj7") is all that matters; individual "voices" or "parts" are of secondary importance at best. This maps well enough to how lute- or guitar-like instruments might be played in an accompaniment role (since these instruments obscure the sense of a "melodic line" or a "part" the most, for a variety of reasons) but music includes a whole lot more than that.
It's very clear that the man wrote chords. It's also very clear that harmony (ie vertical music theory) was not the tool used to write those chords. If you listen to BWV903, for example, there is a long section of arpeggiated chords that defy 18th and 19th century harmony.
The OP's idea of a tritone substitution from Scarlatti does not have the same harmonic function as a tritone substitution in modern music. I would agree with you that if the function matches, you can certainly analyze things in the context of a later theory, but the function does not match.
Finally, figured bass notates intervals, not chords. A crude realization can neglect voice leading in the upper voices, but more skilled realizers of figured bass will preserve voice leading between the intervals in the upper voices. The idea that figured bass is about chords sort of maps backwards the modern abuses of figured bass (which IMO should not be taught as a "basic music theory" subject - but that is for another day) onto the original method.
More broadly, a lot of people like to point out wild 20th century chords in baroque music, but they really didn't think in terms of chords, and as such these pseudo-chords don't have the same function that modern versions of chords do. In particular, Scarlatti was a prolific user of the partimento method of composition, which is a slightly of abstracted version of counterpoint, and his sonatas are pretty good examples of pieces written with this in mind. The method revolves around intervals and movement between voices rather than chords. It's normal for someone thinking in counterpoint to produce some very "modern" "chords" because that's a common consequence of following nothing but voice leading to produce a piece of music.
https://en.wikipedia.org/wiki/Partimento
See also Rick Beato mis-analyzing Bach's counterpoint as containing a very "modern" maj7#5 chord: https://www.youtube.com/watch?v=d1f_tzBx6ko&t=1s