Remember that the original scenario was "raiding the Clans to get Clan weaponry? By the time the C mechs appeared, people were very aware that the Clans had superior weaponry to the Inner Sphere. That's not the freaking surprise you seem to think it is.
If it looks like a Rifleman 3N, and your combat computer says it's a 3N, and it hits you beyond the range a 3N should be able to, that's a surprise. And even if you did suspect it was upgraded with Clan tech, you don't know how it's upgraded. That means you can't rely on what you know about the Rifleman 3N and it's weaknesses.
. . . so you have had the IRL and BTU explanations but not listened?
The original Cs, Atlas/Marauder/Warhammer/Archer/Thunderbolt/Rifleman/Shadow Hawk were done for the Twycross scenario book before Clan secondline designs were ever created. They were given as a means of the Clan forces having garrison equipment for those clusters on the planet that were better than most of what the IS had but not up to the Clan frontline force standard. The authors of that scenario book took the easiest out- they just swapped IS weapons for similar Clan weapons, hence Marauder swapped out PPCs for Clan ERPPCs . . . they are clearly inferior to the Omnis b/c they lack the heat dissipation, even if their weapons are the same. It also made them underweight, but all they did was change a few lines on the RS- the weapon lines.
The IC explanation was the Clans were using up replacement mechs that were being shipped forward but had spare weapons, so they salvaged Inner Sphere machines and replaced the IS weapons with Clan weapons to get something in the PGC/solahma hands to defend territroy- something they were not expecting the warriors assigned as garrisons to need. I want to say it is one of the Aiden Pryde books that has them sitting on Wotan or Sudeten next to a IS salvage/chop shop where the Falcons dropped off all the accumlated salvage from their invasions. Swapping out weapons was the easiest & least time intensive way to get the salvage back into the field.
This is different than the EC refits, which is Star League designs where they were putting prototype or improved weapons on Star League chassis- which already had a higher techbase than the 3025 designs the Invaders used as the starting point for the Cs. They were also more through/thoughtful refits maximizing their capabilities- like the Redback, which is a Maelstrom upgraded by the Widowmakers. Or the Excalibur EC which can be seen as the forerunner of the Woodsman/Timber Wolf/Gargoyle B.
Now in 3145, again IC expediency calls, so we got more 'C' designs for mechs that never had them (but really should have, like Griffin) or 'C 2' (Warhammer, though it has a C 3 too) for those that did previously have those modifications. So, Inner Sphere designs & factories that are using Star League or post-Star League technology have Clan components grafted on to boost their performance though they are once again 'less' than the pure Clan mechs & Omnis. This allows the Wolves, Falcons, and the Foxes who are selling to bulk up the options. IRL, it gave another option for the KS minis to have 3145 versions, a sort of IS & Clan WYSIWYG match.
NOW . . . nothing says the AFFC in 3054 could not make a Marauder C- but why would they really want to? Their new Marauders have DHS, some have better armor, and their secondary weapons are generally better. But you want your PC, who has the old family Marauder to chase down Clan ERPPCs and effectively duplicate what he heard one of his buddies ran into raiding the Clan OZ? Go for it. I would also now however that . . . I think it was the Warhammer? Had one version that was specifically linked to the Dragoons for their production- question is where they refitting it or were the Foxes selling them that way?
I was thinking of the unit lists in Clan Wolf and Jade Falcon Sourcebooks. They include IS and SLDF units but not what variant they are. I'm thinking of the unit lists in the Wolf's Dragoon Sourcebook. They do list specific variants. Some of which didn't originate in the IS. And didn't the Dragoons have to downgrade some of their mechs? I'm also thinking of the Improved Weapons found in TRO:3050. They were considered Extinct then. And there's the fact that the Clans have SLDF Tech.
I was thinking that at the time the Clans were founded, they only had IS/SLDF Mechs. They did produce a few of their own before Operation Klondike but most of what they had were the mechs they brought with them. We're given some rules for adding Clan prototypes but the Improved Tech was around for 20 years or more by the time it ceased being produced. So where are the upgrades? Where's the upgrades to Clan Tech that would have come later? There should have been plenty of upgraded mechs. Fortunately, we have to gotten some but shouldn't there be more?
Since there are (C) Mechs 200 years before the Clan Invasion, were those seen on Twycross really the first time they were used? Did the Clans really go from the Rifleman 3N straight to the Rifleman IIC and then back to the Rifleman C?

Maybe there's an EC in there we don't know about? Maybe the Twycross Cs were rush jobs and they didn't have time to fully refit them? After all, I would think that after 200 years of Clan tech, a Clan Tech would 2 LPLs with only 12 SHS isn't a good idea. Having to get mechs out in a hurry, and mechs being too light and running way to hot, sounds like a rush job to me.
I get why it happened in real life. We got Mechs like the TRO:3050 Panther and Scorpion around the same time too. I also get being lazy. Still, with the retcon adding in heat sinks, I would have thought TPTB would've uses doubles. Especially now that swapping heat sinks can be done in the field? Which makes me want to think they're rush jobs. If that's the case, why not say s? Why not tell us what variant the techs were going for but didn't have time to complete?
And I still wonder about the naming. They obviously started off using letter and numbers with the unit. The IMP-1A Imp proves that. Adding C or EC is okay but it sounds like an IS thing though. Something to call a variant when they don't know the exact name. Like calling a Timber Wolf a Mad Cat. Especially, the EC. Would the Clans put Early Clan on their variants? If that's what the Clans did though, cool.
As for the IS creating C variants, Clan tech is usually lighter and more compact. Many also tend to have greater range and or greater damage than SLDF weapons. So yes, I can see the AFFC making a Marauder C. Clan ER PPCs may not have better range than SLDF ER PPCs but they hit 50% harder for the same amount of heat. They're also lighter which could mean 2 additional tons to use on something else. Besides, after a few years weren't several of the frontline forces equipped fully with Clan Tech? So maybe there is an IS Marauder C? And if C is just added to the existing designation couldn't there be a Marauder MAD-3R (C) and a Marauder MAD-5D (C)?