koobs: It sounds like applying the fix for this bug to the Python 2 branch might satisfy you, right? It only seems to have been applied to 3.5+ so far.

Matt: It sounds like you are trying to pre-compile $(PGEN) for the host, and then rely on it not being rebuilt. Maybe there is a better way, like changing the $(PGEN) command line to use a $(HOST_CC) or something. (I’m not familiar with the build system; certainly not when cross compiling.) But you could also try and identify the dependency that is causing $(PGEN) to be rebuilt, for example with Gnu Make:

$ make --debug=b Parser/pgen
Updating goal targets....
   Prerequisite `Include/Python.h' is newer than target `Parser/acceler.o'.
  Must remake target `Parser/acceler.o'.
[. . .]
 Prerequisite `Parser/acceler.o' is newer than target `Parser/pgen'.
[. . .]
Must remake target `Parser/pgen'.