Maybe it's irrational, and I cannot actually justify it (and of course safe writing is of primary importance), but somehow rewriting the whole file feels like a good thing for a secrets storage. Updating only part of a file obviously reveals something, even though it probably shouldn't matter if it doesn't reveal anything useful. But the default mode of thinking is we can never assume the leaked information cannot be used somehow.
KDBX seems unique in this threat model out of the major providers. The cloud ones all use a relational DB, while major local ones like Enpass & Codebook just use a SQLCipher store. I wish someone with some real experience here would chime in: What metadata does a SQLCipher DB leak that a KDBX file does not? I mention that both of them obviously reveal the size of your vault to an attacker (w/ KDBX reporting the size more accurately, ultimately irrelevant), which is pragmatically unavoidable information leakage.
I do use it, and rewriting the whole file annoys me especially when the storage is not local and the database contains sizable blobs. For storing passwords and short secrets, it makes little to no difference but if I have 10 1MB blobs stored in there, it becomes upsetting.
Well, yes, this is what OP is saying, and I'm not arguing against that. However, this is not what *.kdbx was designed for. And I am only talking about what cryptographically changes for the intended use case if we encrypt every page separately.
