I certainly do appreciate that the file format internals are so well documented here. It really reveals a lot of information about the inner workings of sqlite itself. I highly recommend reading it; I actually saved a copy for a rainy day sometime and it was very insightful and absolutely influenced some design decisions using sqlite in the future.
I assume the SQLite team could increment the version to 4 if they really needed to, and leave the LOC to update (or not) their recommendation, which specifies version 3.
Compared to the amount of SQLite database files in the world only few are shared between different applications. If there is an upgrade path most won't notice. The bigger issue imo is API and SQL dialect compatibility.