I decided to take Pd out of the equation, so I did a quick test using just Tcl/Tk on Mac OS X and Ubuntu Studio. It looks like it confirms what I am talking about: for some reason 12 point is big on GNU/ Linux. So I think we can handle this by forcing 12 point fonts to actually use 11 point on GNU/Linux machines.
Here is the script and the screenshots:
http://pow.idmi.poly.edu/~hans/pdfonts/fonttest/
.hc
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