Is there any reason the ship designs are not researched the same way the missile design are? It would solve a lot of weird behavior associated with modifying a ship design while it is still in service... It also mean the design decision are more meaningful as they cannot be instantly modified.
The one thing that I see as a problem is that a variation on a known design would cost just as much research as the original. Maybe there could be a "Use this design as a base" option that let you edit the design up to a RP limit(based on a fraction of the original RP cost). The new design total RP cost would just factor the new components + a fraction of the original RP cost.
example:(Assuming 30% limit on RP upgrade and 10% fraction base cost)
Valhalla class troop transport MK1, a new design, was designed and then researched for 300 RP
some year later, the troop transport need more space and some upgraded point defense so the MK2 concept is created from the original MK1.
The RP limit is 30%*300, so a maximum of 90 RP can be spent on the upgrade.
It is based on the MK1 so the cost for the new design is a base 10% x 300RP for the original concept+ the new component worth 50 RP
So for a cheap research cost of 80 RP the upgraded design can be retooled and then built at a shipyard...
Sorry if this was already discussed, I might have missed it...