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.
Whole-file encryption with authentication is also more tamper-resistant. Basically the only thing an adversary can get away with there is rolling back the entire file to a previous version.
Whereas, any incrementally encrypted format has the additional risk of piecewise manipulations. For example, while SQLCipher authenticates each page, it doesn't authenticate the entire file, allowing for pages to be deleted, reordered, or duplicated (though duplication is easy to detect since each page has its own IV). The end result will generally just be a corrupted database, which will probably get detected by PRAGMA integrity_check, but compared to KDBX, this will not be detected by default nor is it guaranteed to be detectable at all.