I shudder to imagine the logistics of retooling every LRM factory in the Inner Sphere to that level of sophistication, not to mention having to retrain every mech tech alive.
Going with a Watsonian explanation?
The Clans rolled in at the end of a year long tether and setup factories (presumably to produce cLRMs as well) inside of a decade. Post-3060, at least two of those Clans are camped out within Successor States at any given time and their frontline units are exclusively (or near-exclusively) armed with cLRMs. Ergo, retooling factories in BT isn't that difficult as long as you know what you're doing and the people who (empirically) know what they are doing live right there.
The Doylist explanation is better: TPTB didn't want cLRMs supplanting IS LRMs on frontline mechs for reasons of faction flavor. So the cLRMs... just didn't.
I just look at it as, after 50 years, the Clans still have a massive advantage in tonnage compared to IS models. Why haven't they decided to sacrifice durability etc.in favor of the lighter unit?
Fluff only goes so far, in the face of that kind of advantage.
Fluff is going to be the only explanation. Like you said, a piece of equipment with superiority to the degree that Clan LRMs possess in comparison to IS LRMs
should mean obsolescence for the original.