Not that it helps with the existing frustrations, but @matjaz spoke a bit regarding “undo / history / cmd-z” and the changes that took place in v5.97 in this other thread.
The following is also from the Release Notes for 5.9.7:
Combined Undo history
Until now it was possible to use separate undo histories for each page and CSS styling by enabling it in Undo options. We removed this option, so that now only, the default, combined history can be used. This lets us remove some complexities from the undo system and that will help with improving it further.
Based upon that verbiage it seems to remain something they are aware of while seeking to address and improve things. So hopefully current frustrations will someday improve for users, perhaps in the next major release when it comes.