Chords with accidentals

For what it's worth, I don't have a problem reading accidentals that way but if you want to flip the noteheads easily then [Shift]x does it (and you can select multiple notes before applying).

Rules for accidental stacking (one of the "official" terms used in the music engraving industry) are complex but also highly subjective. So it isn't unusual that different editors will choose different solutions for the same chord, and it's pretty much a given that different notation programs will have different defaults.

That said, I'm not sure I understand your specific concern. For one thing, bar one of "Gloria" uses two voices but not for any apparent reason. If I understand what you are saying correctly, it seems like you did this in order to force the "F" to the left side of the stem and thus be closer to its accidental. But without a musical reason to introduce multiple voices (eg, truly independent lines, or independent rhythms within a single line) , I would claim this was the wrong choice. Changing the notation of the chord just to accommodate accidentals is not normally appropriate. While accidental positioning is indeed subjective, notehead positioning is not - at least not in the vast majority of cases, and this is not one of the exceptions. You can consult any text on music engraving for confirmation of this - Elaine Gould's "Behind Bars" is considered the definitive modern references, but there are plenty of others you could consult as well if you like.

In this case, the normal rules of music notation call for this to be represented as a single chord, which should be stem down, with the "E" on the left and the "D" and "F" on the right. The presence of an accidental on the "F" does not change this.

Similar story for several the other measures here - they use multiple voices for no apparent reason. And the measures that don't are correct as is. In particular, you mention measure 11, which is absolutely correct. The F must go to the right, the sharp to the left even though this makes them not adjacent. This is ont one of the situations where the accidental stacking rules are subjective - this one is black and white. It's only when multiple accidentals get involved that there is room for different approaches. And even then, realistically, with only two or three accidentals, most editors will make exactly the same choice.

The defaults used by MuseScore in cases of multiple accidentals, are, FWIW, pretty much state of the art. We undertook a large project before the release of 2.0 to compare our accidental stacking with the recommendations given by Gould and others, and also against the defaults used by Finale, Sibelius, LilyPond, Dorico (not yet released, but its algorithms were published) to be sure our results were at least good as theirs.

All of this is to say: what MuseScore is doing by default is already correct for your example. While there might be some more sobscure cases involving four or more accidentals per chord where you might need to tweak some things, you really shouldn't be messing the defaults normally, because they are in accordance with established standards.

Ooops, I think i did misunderstand one aspect of your example - there is a musical reason to use two voices in Gloria, because the bottom voice is for pedal only. That's fine, but it's still the case that the defaults used in MuseScore are actually correct here. Which is to say, measure 3 is exactly as it should be. Again, notehead positioning is not supposed to be affected by the presence of accidentals.