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It's less of a problem when building python extenions, where you are probably fine with using "just the same" as the installed python.
However in my case I am embedding python as a scripting language into another application. So there is very few python related code and alot of other code. The python-config script "injecting" unnecessary build flags that in fact even change things (-DNDEBUG) is very annoying as it changes all the non-python code too.
A simple thing like the --includes that just outputs the -I flags would be the best solution IMO. But to have this working you would need to have a guarantee that there is no actual code in the form of #define / inline functions in the headers which potentially breaks if you use different flags from the python library. In fact --includes is what I am using now, I just hope that I won't hit any of the preproc macros by accident...