3.5 to 3.0 was the exception though, more like AD&D to B/X.
I've heard 3.0 to 3.5 compared to AD&D 1e to 2e, since that's actually kind of a fair comparison. Nobody ever really talks about "AD&D to B/X," though, because B/X wasn't based on AD&D, it was based on Holmes Basic and the white box (and Greyhawk).
The incompatible differences between B/X and BECMI or RC are that thieves skills advance slower (there might be specific other differences like xp charts or whatever, but I never checked and used material from BECMI and RC era basic in my AD&D games as I had B/X stuff). I would expect to use a Merchant Prince or shaman class from the later Gazetteer series directly in a B/X game without mechanical conversion issues.
There are a bunch of little differences in the attack roll tables, saving throw tables, XP tables for certain classes (thief comes to mind), spell tables (cleric and elf), and of course the vaunted thief skill progressions. But it's hard to call them an "incompatible difference" when the changes to thief skills were made after
the 1983 printing of the Mentzer Expert Set, which conforms
to the to the thief skill table in the 1982 Cook Expert Set
. The thief skills weren't stretched out until after the Companion Set was published, and then the Expert Set was updated to match in 1984.
In short, if B/X and BECMI are different and incompatible editions because of the thief skills table, then the 1983 Mentzer Basic and Expert Sets are part of the B/X edition and not the BECMI edition. (I think the more defensible position is that Classic D&D is one game that was gradually changed in small, piecewise increments between its debut in 1981 and its twilight in 1996.)