A - it's been there for about 3 years, version 6.?, I've not seen anyone complain about it until now.
B - I don't use the main toolbar so the Undo sits on the Find box, but it doesn't stop me typing there.
C: you could move the Find Duplicates, as @dunhill suggests, either within the Main toolbar or to another toolbar/menu, or access it via the All actions menu (default shortcut is Ctrl/F1) or give FD its own keyboard shortcut
D: you could request an Enhancement, see 4th para ==>>
https://calibre-ebook.com/bugs
Aside - a better position for it would be on the Title Bar, but MacOS may prevent that.
BR