I don’t think you should need to change the Vertical Spacing values for projects with multiple flows; indeed, it’s already the case that within a single flow you can have systems with wildly varying numbers of staves, and it’s not necessary to change those values to accommodate those systems. In general what I would suggest is that you set the values such that you are allowing justification and not the ideal gaps themselves to do the heavy lifting: in other words, set the ideal gaps to the smallest values you can, and then rely on vertical justification to spread the music out correctly.
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