A compromise: like someone was suggesting earlier, any change made in-game will cost CBills. But, any mech made in the out-of-game editor just has its formulaic price.
I.E., I make a shadowcat variant with, say, a CUAC20 and flamers in the mechlab. It costs whatever the cost of the chassis+systems+armor+weaps is. But, after a few deaths, I decide that some SPLs would be a better choice for those slots. If I change it in-game, when I change it it costs me (price of SPLs + price of whatever else I change) * 1.5 or something, at the instant I make the change.