I think I know it fairly well.
Well enough to know that Secret Weapon is not a normal negative skill.
Pick any Star Player with Secret Weapon. Any of them. Add 30,000 and see if that looks like a fair price to use the player for the full game.
Let's take a specific example. Zzharg Madeye. Based on a Chaos Dwarf (70,000). He loses Block, but gains a point of STR and a point of AG, as well as two regular skills and two double skills. He costs 90,000. Using your method, he should cost 180,000. (70,000-80,000+190,000). But, you know, you can usually only use him for half of the game at best, so his price is vastly discounted.