I'm quite certain that the makefile is generated before the "make"
program is launched in separated process. Follow is the original code
where the makefile is created (line 14) and a task is put in queue (line
19). It's executed in the main thread (no parallel execution here).
There's no way that the process is launched before the makefile generation. 
 
01    for Module in Pa.Platform.Modules:
02        Ma = ModuleAutoGen(Wa, Module, BuildTarget, ToolChain, Arch,
self.PlatformFile)
03        if Ma == None:
04            continue
05        # generate AutoGen files and Makefile here
06        if self.Target not in ['clean', 'cleanlib', 'cleanall', 'run',
'fds']:
07            # for target which must generate AutoGen code and makefile
08            if not self.SkipAutoGen or self.Target == 'genc':
09                Ma.CreateCodeFile(True)
10            if self.Target == "genc":
11                continue
12   
13            if not self.SkipAutoGen or self.Target == 'genmake':
14                Ma.CreateMakeFile(True)
15            if self.Target == "genmake":
16                continue
17
18        # Generate build task for the module which will be launched
separately
19        Bt = BuildTask.New(ModuleMakeUnit(Ma, self.Target))

I think the Py_BEGIN_ALLOW_THREADS and Py_END_ALLOW_THREADS should not
be used for fsync in the Python core code (in posixmodule.c, right?).
Because fsync is mostly used to solve file operation issue in parallel
execution context, it should not give out CPU time to other threads or
processes when it's running.