Keep workbooks independent - because they are from a user perspective
If you really want workbooks to all live in one process the user shouldn't know about it. They shouldn't share anything - undo buffers etc. should all be independent. Easiest would just be to bring back the option to have every workbook in a separate process - it made sense to everyone and was easy to understand the behaviour.
MS has provided a partial solution. With the /X option when opening Excel files, you can force it to start in a separate instance/process, and then you can open your file in that instance. Unfortunately, this is clunky in that you must remember to open each file via this two-step process - if you open a file in Excel or via File Manager or via a right-click on the icon, Excel will put the file in one of your existing processes.
As to Thomas K's comment, I don't care as I am a simple user and never link across files/workbooks only across worksheets in one file. So, it is not worth the pain of the current approach (one undo buffer and one Find/Replace window across all files).
Thomas K commented
There could be issues though, what if two workbooks are linked and you undo something in one of them that has some influence in the other, then the second workbooks 'undo stack' could be kind of broken.