You are aware that all of those masks have holes directly in front of the thing they're supposed to be blocking?I take it you didn't follow the link I provided earlier then, because it has solutions for basically every potential problem you brought up (images from http://www.unitedsound.org/mask):
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This prevents the brass players from spraying spit around themselves from their mouthpiece.
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This bell cover prevents "aerosol spray" from coming out the end of the instrument.
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A version of this for every woodwind instrument would prevent spit from spreading after coming out of the holes in the instrument.
Like I said earlier for clearing spit from brass instruments, a process where the musician leaves the stands and goes to a designated area alone to clear their spit into a deep sink or garbage can and then disinfect their hands and the outside of their instrument would prevent spread from clearing their spit.
Now you did point out 1 potential problem that isn't explicitly covered, flutes, as they have a gap between their mouth and the mouthpiece. However I believe you could likely modify the first mask shown above in such a way to accommodate that and still allow the instrument to be played.
What about any of that specifically won't work?
A mask with a hole in front of the mouth isn't a mask.