The issue is that here we are shadowing with an alias a primitive C
subr.

Compiling speed 2 the assumption is that these are not redefined or
advised (the manual warns about doing that).  Function calls to C
primitives at speed 2 are hardcoded for performance reasons in the
generated code.
 
 We have a customize listing exceptions for that
`comp-never-optimize-functions'.
  
You should solve the issue adding `yes-or-no-p' to this customize and
recompiling.

 Ah I see now. This makes sense, although also makes it harder to configure.

On the other hand customizing `comp-never-optimize-functions' will solve
the issue only for external packages because you likely already have
compiled the whole Emacs with the default setting...

IIUC I may need to modify the source code of the `comp.el` file, because it gets used when doing `make`? 

--
Best regards,
Andrey Orst