Basically, yes, you are correct about how IS Mechs are customized, it takes money, time and trained techs, and in some cases, specialized facilities. However, if you have enough money and time, ANYTHING can be done. It IS a pen and paper game after all, rules are there to be ignored or used as seen fit by the players, general rule with customization of IS Mechs, if you've got the money, consider it done. I once created a brand new Mech, customized from the internal structure on out, complete blue prints, my GM was a stickler for stuff like that, we were all in college and had access to CAD software, and so on. He took it, looked it all over, did the calculations for the work, gave me an amount and time frame for a prototype to be developed, tested and delivered. I gave over the cbills, and our next game session I had my brand new fresh from the testing grounds Mech. Even in PnP, time is something that's only important when it actually needs to be important.
Sure, it'd be great if they did that in MWO, make us WAIT for months to customize our Mechs as we want. I think this game would have never gotten off the drawing boards if they did that. Stock only is one thing, but allowing for customization at a cost of serious real world time, not going to happen, not if they want to actually make money off the game.
OmniMech construction rules are real simple. If it's not an Omnipod, it's static, doesn't get changed, the entire basis of the Omnipod system is built around the fact that ONLY certain things get changed, the Internal Structure doesn't get changed, engines stay the same, certain components are hardwired and that's how they work. Omnipods are specially designed pods that weapons can be fitted into and all use special connectors to hook into the Mech's computer and control circuitry, so you can't go mucking about with the structure of the Mech or it's engine, the hardwiring of those isn't something you do in a matter of hours, which is the selling point of the pods. Drop on a planet, see that the battleground is useless for LRMs, too hot for lots of energy weapons, so swap out those LRM and ERPPC pods for some ERML and uAC10 pods, done in 2 hours. IS Mech, you drop and see the same battleground and well..uhm...yeah, you go into battle with whatever you showed up with, you don't get to swap them out in the field like OmniMechs can.
In MWO, it doesn't seem like that much of an advantage, but it is since Omni's have X tonnage in pods, and MOST OmniMechs can pretty much cover the gamut of possible weapons. Some obvious things like the Nova not being able to mount LRMs, glaring issue that should be addressed, ALL OmniMech should be able to equip ALL weapon types, and they need to redo some of them like the Warhawk which should have better configs possible.
Clan XL engines and ST's being blown off, there SHOULD be a penalty, you've just lost a chunk of your ENGINE for Kerensky's sake, come on! The entire engine doesn't shutdown like an IS XL does, but it SHOULD be a very obviously bad thing when you lose THAT much of your engine, 2/3rds of it for all intents and purposes after all. 20% drop in speed, 20% decrease in cooling ability, seems pretty tame really, since the actual TT rules are much harsher, 40kph drop in speed, 1 heat/second gained. Most Clan Mechs won't see 40kph drops OR gain 1 heat/second with the ST blown off. Dire's will see around 10kph drop, KitFox or Adder will drop around 20kph, Scrow and Timby around 20kph as well isn't it? That is a DROP of 10/20kph from their TOP speed, not being slowed DOWN to 10/20kph top speed. It's far from being instant death, most people won't even realize it, same as most people didn't realize they've already been losing that cooling ability....
2 out of 12 crit slots is not 2/3 of your engine...in fact, it is merely 16%