I would argue LWW is the opposite of a merge. It is better to immediately know at the time of writing that there is a conflict. CRDTs either solve or (in this case) don't solve a problem that doesn't really exist, especially for package managers.

Git solves that problem and it definitely exists. Speaking of package managers, it really depends. Like, can we use one SQLite file for that? So easy, why no one is doing that?

idk, debian for example uses plain text files. I have to imagine it would bring some advantages to move that over to an sqlite to improve performance, but then it seems package management designers fall into the two categories of either under-engineering or over-engineering the solution. There is little glory in evolving something incrementally, everyone wants to do green field stuff.