I think it's good that we're running into this issue now, as opposed to when the MechLab is in. One of the problems (I imagine) with pricing 'mech components is that the CBT prices were partly based on the setting: advanced electronics, including systems like C3 which were appearing in real military units already at the time they were introduced to BT, were overpriced due to their supposed scarcity in the fiction. Some highly effective weapons or components could no longer be constructed due to the loss of some key component's factories in the fiction, leading to inflation of that specific price, while other equally effective weapons were cheap because they were still widely made. So adjusting MWLL component prices based on in-game efficacy makes a lot of sense to me. This is one place where I think CBT should be completely tossed aside.
I would suggest that weapons, at least, should be priced based on a variety of factors, such as range, ammo, flight time, DPS, impediments to use (lock-on, overheating, minimum range) and so on, but weighted heavily towards DPS and range adjustment. The cost of the base chassis can be computed from its own components, but the final cost should be adjusted based on the total efficiency (say, by multiplying by a factor for each component that makes all the weapons or all the equipment function better, such as double heatsinks). There can be a subtractor or divisor applied to the weapon package for each separate range envelope over 2 (causing multiple weapon groups), say, or factors for MASC and for DHS could be included last since they enhance both threat range and overall DPS output. I think with some thought the automatic pricing system can be made to work.
The missing piece, though, is reporting and tweaking. The players don't really have any way of directly adjusting the prices of configurations, or of providing concise feedback to the devs on possible adjustments. Without knowing the details of how different components are priced it's hard to even begin to make suggestions, except things like "Mech X Alt Config B is totally broken!" or "I can't afford Mech Y Prime even though the cheaper Alt Config C is much better." Which is not to say that these aren't constructive, but I feel like we could do more to help the devs tweak the prices if we knew more about how the prices are determined right now.