since the Makefile.pdlibbuilder is the canonical documentation of itself (it has plenty of comments explaining its workings), i guess this is just the answer.
make PDINCLUDEDIR=/usr/local/include/pd
That did it (I guess you'll think "obviously" :) )
(i guess pd-lib-bulider could prefer /usr/local/include/pd over /usr/include/pd, you could create an issue)
I'll do that. Thanks for the help.