I see the problem, your numbering scheme doesn't really lend itself to divergence on a per-platform basis. I wouldn't beat yourself up about this as there is no obvious elegant solution (as far as I can see). The important thing is that users can distinguish between the two functionally equivalent 1.36 versions.
You could introduce a 4th digit group for patch level, i.e. go to 1.36.0.1 on mac. Or you could introduce some kind of suffix (like rc1 for release candidate1, fp1 (fix pack1), dr1 (defect resolution) or just the more neutral upd1 for update).
How about geany-1.36_osx_upd1.dmg ?