Not a problem for XML per se (you can work with byte positions, and with fixed-size blocks to avoid resizing/relocation), but in the case of KDBX there is the issue that it is encrypted as a whole. Not encrypting as a whole, on the other hand, risks leaking more information about the contents, like you can see which parts/how much changed between one update and the next.

I actually prefer this. It's how most user-facing file formats work. KDBX in particular is often used in conjunction with syncing software, and I don't want a half changed file to sync and then the connection to be lost. The usual paradigm of "write new file then move and replace over old file" works more safely for atomic changes.

That's not a feature, that's an implementation detail.