Honestly, how is this allowed?

[Avoidy]

I'm convinced they care more about the sub money these people provide then the RMTing they're doing because it logically would not be even remotely difficult for them to trace the gil and notice suspicion transactions.

This is it.
That person who owns all those houses has dozens of accounts for this purpose and each of those, I guess, is paying a subscription. They probably RMT the gil and then use the real money they get from farming gil to pay the sub fees as well. Tracking this sort of thing wouldn't be hard at all, but there's a financial incentive to just do nothing.
Submarines were a mistake. They print money and let certain players amass wealth without actually engaging in the multiplayer economy. They also drive a lot of real money trading. There's no good reason for subs to exist, but it probably keeps people subbed (don't wanna lose your house, which you need for your subs, which you're invested in) which is why it stays in the game ruining housing and FCs and gil value while something comparatively harmless like coffee biscuits get nerfed into oblivion.