> the entire point of Free Software is to allow end users to modify the software in the ways it serves them best

Yes?

> completely counter to his own supposed raison d'etre

I can't follow your argument. You said yourself, that his point is the freedom of the *end user*, not the compiler vendor. He has no leverage on the random middle man between him and the end user other than adjusting his release conditions (aka. license).

I'm speaking here as an end user of gcc, who might want e.g. to make a nice code formatting plugin which has to parse the AST to work properly. For a long time, Stallman's demand was that gcc's codebase be as difficult, impenetrable, and non-modular as possible, to prevent companies from bolting a closed-source frontend to the backend, and he specifically opposed exporting the AST, which makes a whole bunch of useful programming tools difficult or impossible.

Whatever his motivations were, I don't see a practical difference between "making the code deliberately bad to prevent a user from modifying it" and something like Tivoization enforced by code signing. Either way, I as a gcc user can't modify the code if I find it unfit for purpose.