You can limit the problem by only using prototype engines and weapons on that ship.

But the two things that are going to be annoying with increasing technology is capacity and range.

There is no prototype range component..... there should be!

If there was a prototype range component, i would be happy with that, problem solved.

I had noticed other funny thing. Any ship (with acceptable hull) can be upgraded to the design with One-Per-Faction component if there are no ships of this design.

But also you can actually upgrade all ships of some design to the design with One-Per-Faction component at the Govern screen. And all of them will be upgraded, so you can get a lot of ships with powerfull components.

You should decommission ship with One-Per-Faction Component, because if you upgrade it to the core or custom design (without One-Per-Faction Components) the game will still count this ship as one that have One-Per-Faction Component.

...and this is not so funny thing. A bit flawed DLC.

It's not so much bugged as not accounted for, upgrading uses a different system, that dose not currently account for unique component. I will see what we can do to make it support it. 

It might have to wait for Crusade, but I will see if we can get it dressed before that.