Ever since s-mods became a thing, I wasn't a huge fan. And now this change, my first reaction is also negative. I believe Alex will make things work in the end but here's my thoughts why this was too much spent dev time.
So, s-mods are basically old Loadout Design where they're meant to give your ships some extra power, just instead of adding pure OP points, you get those through free hullmods (that you can't remove). Which wasn't the most elegant idea, but hey it works. Now, there were discussions on how the most expensive hullmods always get built it. I understand those but since I always viewed it as just bonus OP, I felt it was fine. I mean you still had to think which specific hullmods you want forever.
Doing this bonus-nothing-penalty mumbo jumbo will increase the time in the refit screen big time. When in the end, the final product will remain pretty much the one you were going to build before this mechanic. Obviously with some bonuses and penalties on the side. The argument "if you don't want the penalty, build in something else" is sooo bad. So you want us to spend story points on something we DON'T want, so we can get something we DO want in the end. That sucks. Ok sure I'll s-mod ECCM instead of EMR, that's the solution. And it took who knows how much time to come up with all the bonuses and penalties.
Again, I understand why Alex is doing this, but it seems like an unnecessary mechanic just to get out more min maxing out of people. Although no point in arguing since it's coming in the next update, we can only hope it turns out fine.
Btw can't believe there's a problem with s-modded EMR and Heavy Armour while SO is still a thing in the game. The single most braindead part of the game.