In my experience, the performance bottlenecks in bioinformatics is usually IO, parsing, de/compression and needlessly slow algorithms. You rarely get meaningful speed improvements by internally encoding the sequences one way or another (storing small fixed-size sequences in machine integers is an exception). There can be other advantages, though, like reduced memory consumption.
Partly for that reason, most DNA data is just stored as gzipped text files.
The « slow way » of the post would also count matching code units which is utterly useless, really.
Fuzzy matching is another aspect that comes to mind.
Heck, if your usual encoding is UTF-8, the flag bit can be purely advisory and ignored when it doesn't matter.
And if we’re already down the “write it understandable and trust the compiler” path isn’t that the better way to go?
It’s interesting to me that C is now effectively a “higher level” language than it may appear on the surface because of optimization by compilers.
In all cases, obviously the real magic is in the 64-bit word comparison routine (which doesn’t get more than a passing mention); converting the former problem into the latter is extremely straightforward and obvious - if you know that optimized solutions for the latter exist (I personally didn’t know of this bit twiddling hack (aside from doing it via SIMD, obviously) and am grateful to learn about the approach in Muła’s code).