Um... the mods don't make a difference, the armor type makes a difference. If you have a piece of heavy armor and a piece of medium armor, both with the exact same armoring, mod and enhancement, the heavy armor will always give you more armor protection. There isn't a way to offset that armor protection loss. If you can live with the lower armor mitigation then it's all good, I guess it depends on your advanced class/play style.
As a merc pyrotech I always use Mako as a companion and I could probably get away with one or two pieces of medium armor in PvE, I would never try that stuff in PvP though... of course you're probably going to get stomped as a mercenary in PvP anyway, so in the end it still wouldn't matter.