Because, as reikonomusha put it in the previous comment, "you can edit, insert, splice, overwrite, etc. to your heart's content in your favorite text editor", which makes the overwhelming difference. You don't see the notation as you're entering it, but you have a way to iterate on that.
However, it greatly helps if you're a developer or computer scientist, since you're working with a compiled markup language.
LilyPond isn't the answer for regular mortals.
LilyPond has sane playback. If the piece you've written is 3 bars long so far, and you play the MIDI file that pops out of the compile, you hear 3 bars and then it terminates.
MuseScore requires you to specify the number of bars before you compose and then gives you sheet full of that many empty bars. When you click play, it plays through all the notes you have composed so far ... and then doesn't stop! It goes through the empty bars. It's like the Forrest Gump of music programs. Run, MuseScore, run! If you put a double bar in its path, it doesn't get fooled: that's not the actual end of the file, so it blows right through it.
What is a problem for me though is that the measure properties dialog opens up behind the main window...
You're talking about a right click context menu which has a Measure Properties command. That indeed opens behind the main window. (Is this using GTK+? I regularly see this issue in GTK+ programs on Windows like GIMP; it's been there for at least 15 years.)
I see that I can set the actual time of a measure to, say 1/4 which creates a one beat pickup measure if it's the first measure.
The weird thing is that the software can do this but they've made it so difficult and fiddly via the UI that it's impractical as part of any work-flow but there is nothing fundamental/technical preventing MuseScore from supporting this way of working.
The forums are generally hostile when (new) users innocently ask how to use the software this way - perhaps out of fatigue.
It seems it's been decided that the "one true way" to transcribe music is know how each note relates to the bar structure of music first before adding anything to your score. As a result it feels like trying to use a word processor stuck in overwrite mode.
(The use case I need this for us when I want to transcribe music by ear. I first use my MIDI device to type all the notes, and subsequently modify the lengths. Currently I have to cut, modify length, paste, repeat. For every, single, note, rest… Extremely annoying)
If anyone knows software that can help me with this, or another way to transcribe music wrt my use case, let me know!