The mark color is saved in the lib and is actually changing the font data, so it makes sense that the save state of the document will update.

There are some options:

set the change count of the document to zero after changing the font data, just be careful with data loss, of unsaved fonts

from AppKit import NSChangeCleared

font = CurrentFont()

for glyphName in font.selection + font.templateSelection:
    glyph = font[glyphName]
    glyph.mark = (1, 0, 0, 1)

document = font.document()
if document:
    # set the document change count to zero
    document.updateChangeCount_(NSChangeCleared)

Adding an L or N (for glyph.note) is a bit more difficult cause you have to overwrite the defcon representation factory generating the glyph cell.
Adding smart sets is probably the easiest.

But I guess your proposed solutions are not the best options for the problem…

however, good luck!