I've tested this under Matlab R2009a and Win7/64. I get equal fond sizes for 12 and 13 point. The problem does not depend on the renderer, but with a higher resolution the fontsizes differ:
print('test', '-dpng', '-r300');
It seems, like the fontsizes are divided by the resolution and rounded to the next integer value. I'm not surprised that pixelated fonts are not available in 12.4 point.
In consequence the problem is the expectation that "print -dpng" exports the fonts as you like it. Exporting to EPS and letting GhistScript render the output to a PNG might be better.
But the problem of the truncated lines for Macs remains: I guess that the font sizes are rounded to the next integer, but the available extent is not.