First read the bsd.port.mk file (which may be found in /usr/share/mk/) and the associated bsd.port.subdir.mk file. A lot of the weirdness can be explained properly in there (most of the current weirdness is due to the lack of assumptions about anything, which is necessary due to the generic nature of these files). Also check that you have an up-to-date copy, as the file can change from minute to minute. The most up-to-date copy can be found in:
ftp://ftp.freebsd.org/pub/FreeBSD/FreeBSD-current/src/share/mk
If you find that you still need to go in there and alter things, by all means do so, and then send the diffs to ports@FreeBSD.org if you'd like them to be a part of the default distribution. Please also remember that any changes must respect backwards-compatibility with any and all older Makefiles, unless you want a real nightmare of /usr/ports munging ahead of you! Large scale changes will generally not be warmly welcomed unless all the existing makefiles work without alteration. Sorry!