They are indeed compatible, as are most modern music-notation programs. You can transfer music between them using an open standard called MusicXML. But MusicXML isn’t 100% lossless, so you might need to tweak your music upon importing into a new app (mostly presentational stuff).
Whether MuseScore is better likely depends on your exact needs. What’s your end goal — preparing music for printing? Just jotting down ideas? Composing and hearing high-quality synthetic sounds? Creating instructional material? Sharing stuff easily online?
Thanks for the feedback. I am embarrassed to say it but you asked: I can't read music very well and I like to use NoteFlight to play back scores that I type in to me, so that I can ensure I'm practicing them correctly. That's about the sum total of my usage so far. And I'd prefer to use free software all else being equal.
No need to be embarrassed — we all start somewhere!
In that case, I think you're fine with Noteflight or MuseScore. If I were you, I'd play with both and choose whichever one you feel is more intuitive.
You might also give Soundslice a try (https://www.soundslice.com/) — it has a web-based music notation editor that has practice tools built in (like a visual piano keyboard to show you where to put your fingers).
It's free to use for your use-case. And though it's not open-source, it was developed by one of the people who created the Django web framework (me!) — so maybe my past open-source work counts for something.
Whether MuseScore is better likely depends on your exact needs. What’s your end goal — preparing music for printing? Just jotting down ideas? Composing and hearing high-quality synthetic sounds? Creating instructional material? Sharing stuff easily online?