I am not convinced that the minimal patch would work for my original issue. I wanted to be able to override the -march option which shows up in OPT on Fedora. I was cross-compiling to a target architecture that does not support the -march option so I would not be able to provide a different one as override. 

The proposed minimal patch would leave the OPT value and make it unchangeable because CFLAGS would pull out a value for OPT from the Makefile which shows as in my current Ubuntu system:

OPT=        -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes
BASECFLAGS=  -fno-strict-aliasing
CFLAGS=     $(BASECFLAGS) $(OPT) $(EXTRA_CFLAGS)

The debian-sysconfig-flags looks the most correct because it allows override at any point by emulating the CFLAGS = $(BASECFLAGS) $(OPT) $(EXTRA_CFLAGS) logic.

It still looks like it needs an override for EXTRA_CFLAGS and the logic for LD_SHARED looks wrong. In the Makefile LDSHARED is just:
LDSHARED=   $(CC) -shared -Wl,-O1 -Wl,-Bsymbolic-functions

Why does LDSHARED need CFLAGS and CPPFLAGS? When provided as an override but not in the Makefile? Do we need to allow for this override in the case of overriding OPT, BASEFLAGS or EXTRA_CFLAGS?