Many people are able to compile for 64 bit just fine.
Based on my google search, what you're looking for is something specifying -march, -mcpu, or -mtune with an inappropriate value for 64-bit support.
Here's a likely candidate from the makefile in zone. I didn't check any others.
COPTS=$(WFLAGS) -O -g -march=i686 -pthread -pipe -D_GNU_SOURCE -DINVERSEXY -DFX -DZONE $(DFLAGS) $(MYSQL_FLAGS) $(PERL_FLAGS)
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