I posted this in hopes that consideration for these issues will be given while improving the engraving capabilities in future versions of MuseScore. As you can see, almost everything can be worked around but much of this should be either automated or easier to do.
I've been working on transcribing a complex piano score into MuseScore from https://imslp.org/wiki/Mirages%2C_Op.70_(Schmitt%2C_Florent) (#21581). I have been saving it as a work in progress to my account at https://musescore.com/user/6105546/scores/6325818. This score is still under copyright in the EU so it requires a pro account to download. I always use the measures you get to when you use ctrl+f to make it easier for you to find them
This has brought up several engraving issues that should be addressed in future releases of MuseScore. I have only mentioned one place where each issue arose. Most issues are repeated throughout the score.
m1 - There is not a good L.V. tie that will look good in MuseScore so it's necessary to put grace note after and make it invisible piece by piece since it's impossible to select an entire grace note and make it all invisible at once
m2 - Take out the spacer and see the beams crash into the treble clef on staff 2
mm3-4 - take out the spacer select each of the 64th note beams and press ctrl+r (to reset them) and see them over lap notes. They should avoid notes and put extra space between the staves by default.
m11 - I had to use a voice 3 note to make the L.V. tie on the A1. When I added the grace note after it ended up on top of the main note rather than offset to just before the next note/rest as in other places. I'm not sure what causes this.
m12 - It's necessary to put invisible rests on the other staff in cross-staff notation to have the clef show up in the correct spot.
m13 - Note: don't worry about the invisible sb and se in this score, they are necessary for the person converting this score to braille. I understand it's a limitation of the conversion program rather than MuseScore.
m14 - Cannot create the time signature (Emilio is working on this, hopefully it will be merged into 3.6)
m18 - the 2 note slurs in voice 1 of the second staff had to be flipped to show up in their current (logical) position. This is due to the voice 2 note.
m23 - staff 2, such trickery with voices and invisible notes is necessary for beams like this
m24 - I could have repeated the same process as I did in m23 to make the beam bend but this was close enough for me.
m26 - staff 1, it should be possible to put a white background behind clefs for cases like this.
m35 - more trickery necessary for the beams but they're still not right and impossible to get right.
m40 - The E7 has a forced natural on it. I agree this one should be an e-natural and these should always have an accidental on them to avoid misunderstanding but there are too many scores where this is not made clear. I could have made the rest invisible but think the courtesy belongs. Having said that, the user should be permitted to make the final decision. The note on page 1 actually declares this should be an E# without an accidental, but I believe this is an editorial oversight.
m44ff - though I'm sure the 16th notes in the triplets are precisely placed according to a sound mathematical forumula, they are aesthetically ugly and could be confused for the bottom part of a chord with the 8th notes above the beam. Compare them to the same rhythm in m47ff
m50 - it was necessary to flip the ties from the grace notes to the main notes.
m71&72 - this isn't exactly engraving, but it would be very nice for re-pitch mode to work on grace notes. The rhythms are identical in staves 1 & 2 and it would be nice not to have to reenter all of the grace notes but rather use re-pitch mode.
m76 - staff 2, this is a mystery to me. I'm willing to consider better ways to notate this.
m84 - it was necessary to put notes into voice 2 of staff 2 rather than voice 1 of staff 3 because you cannot cross-staff from staff 3 to staff 1.
m88 - the f# with a courtesy accidental should be an F# not an F natural by default since it's on the other staff.
m123 - the tremolo can use some work
m178 - the bracket shouldn't extend below the second staff. Emilio has PRs to fix the other cutout issues
The remainder of the score is rather repetitive.