Nope, not finding anything that will make an Sci dirty while adding nothing to the undo stack. Nor can I find anything that lets me remove the last added item from the undo stack while not affecting Sci_GetModify status.
I suppose one could create a new setting, pSed.BookmarkCount, which tracks the number of bookmarks in each Sci. Then, in the 11 places where the following (or some other SCI_GetModify statement), is used, modify the code something like this ...
If SCI_GetModify(pSed.hEdit) Then
would be replaced with this
If SCI_GetModify(pSed.hEdit) or pSed.BookmarkCount Then
Since each bookmark (Ctrl-F2) adds an apostrophe to the undo stack, if I were doing lots of bookmarks, I might argue that the coding effort would be worth it.
But, I rarely use bookmarks, so it's not a priority for me.