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On Linux, it is common to include debug information into
every  library and executable; in particular, it is common
to install python with debugging information. This is
possible since debugging information can be combined with
optimization almost seamless in gcc (distributors often
strip the debugging information, though).

So you use Py_DEBUG *only* when you want to do the refcount
debugging. You have to configure --with-pydebug for that,
and you never do that in the wild. *If* you would install a
pydebug binary, you would use a different --prefix, so that
it would not interfere with the standard installation.
Depending on which pyconfig.h extensions pick up, they would
then be suitable for use with one or the other installation.