Generally you should stick to the options that ports provide, whether through the 'config' target or the -DWITH_FOO knobs that Robbak mentined. The CONFIGURE_ARGS variable should get passed onto ./configure when a port uses it, so # make CONFIGURE_ARGS+="--custom-args" would likely allow you to modify the configure arguments used for the port directly, if the port Makefile doesn't give you proper way of controlling he build options you need (for some odd reason). Generally there should be no need to manipulate the configure script directly.
When in doubt or curiosity about what something does in ports, open /usr/ports/Mk/ and start reading. Best way to find out, even compared to the manual!
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My Journal
Thou shalt check the array bounds of all strings (indeed, all arrays), for surely where thou typest ``foo'' someone someday shall type ``supercalifragilisticexpialidocious''.
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