I guess I miss what you're after. If I enter a whole note in layer 1, and fill layer 2 in the same measure with hidden 16ths, the hidden 16th notes. With "Affects Music Spacing" checked for layer 2, the 16th notes have an effect on the spacing (no matter what kind of spacing I use). If I uncheck this, I get the behavior you describe, with all the small notes piling up.
Is it possible to re-space hidden notes with Notespacing?
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