It just strikes me as odd to say that the fiction don't really show that omnis can be customized when the place we've seen the most customization is the fiction. It's like arguing that the novels don't show enough 1st person POV, when they certainly show a whole lot more than sourcebooks, TROs, etc.
Oh, I don't think anyone here is arguing that Omnis
can't be customized.
I think what Hellraiser is talking about when he says '
Its an Omni, so it can do anything" arguments' is the occasional time I've seen people suggest that they can personally customize every Omnimech in their force because, well, Omnis are very easy to customize.
E.g, Two Clans players square off with a mixed Trinary on Trinary. One player is using stock configs for his 'mechs- A Timber Wolf B here, a Stormcrow C there, an Ice Ferret Prime etc. with his Elementals using 'standard' weapons. A Point with Small lasers, another with Flamers, another with Machine guns etc.
The other player has all ten 'mechs with his own, personal configs for the Omnis. "Timber Wolf Mega Death" and "Warhawk Ultra Death", all of them using a mix of pulse lasers and streak SRMs. His elementals tricked out with various weapons using the 'modular' weapon mounts.
The fiction seems to be somewhere in the middle, with most Omnimechs using an established config (such as the Prime, A, B, H etc.) while the odd Omnimech (such as the Star Captain's) may have a personal, customized, loadout.
The RPG backs this up with the 'Custom Vehicle' trait if I recall correctly.
EDIT: And just to be clear, the MUL stating specific configs for each Clan shows a preference for certain configs over another, backs up that view in a sense. It doesn't mean a Clan Star Captain can't use a personal config, or even use a personal config that matches a config not listed on the MUL. It does seem to suggest, however, that most Clan warriors typically use established configs which are more or less popular depending on which Clan you have.