Don't know how I feel about the 2 industry slots solution but current Commerce with the new domain item is absolutely broken. The stability penalty is nothing even combined with the free port penalty. I was wondering why I was making so much monthly money in my playthrough compared to before and found out that just one mining colony (with SP upgrade but no domain item on mining) with Commerce (with no SP upgrade but domain item installed) was making more money than everything else I had combined at all times (not tied to a commodity situation in the sector).
As for opportunity cost, I don't really feel like spaceports (megaports, really) need it. It's purpose is to boost accessibility, it boost accessibility. Not everything needs questions and consideration, there's enough of that with colonies as is.
The opportunity cost of Megaports should be some kind of upkeep. Right now you just upgrade to Megaports everywhere by default (even if base accessibility is high, it counters reductions from other sources) because there's no reason not to. It's like if every tiny country on Earth had airports the size of LAX.
There's hardly any thinking or choice required with colonies as they currently are in vanilla, even with the limitations on some domain items. You follow the same cookie cutter flowchart in your head and then it's infinite free money that fluctuates some based on wether you have the items yet or not. Even when money sinks will be added later, the way the money is generated is not interesting and too ez.