[Suicide Junkie]

Every time you have to go through another intermediate hull design, the price of doing a retroseries jumps.

The 50% limit is good, if not a little high.
You can retrofit three or four upgrades at once before you have to pay extra.

Completely rebuilding every component on a ship should definitely cost you a lot.

It can be pesky if you're not ready for it, but all you have to do is remove components from your end design, reducing its price to 70%, and then save that new design as the intermediate retro.