And this is exactly why a PLEX system would harm RMT. Suddenly, players that would buy gil from RMTers have a new, safe option to make gil, and buy that instead, causing RMTers to lose revinue. Not only that, because the scrolls are influenced by the market, undercutting (and by the gods does FFXIV market have a lot of undercutters) would ensure that profits go down further for RMTers. This is because it assigns a market established worth to gil, and they'd have to compete with the entire player base to stay in buisness. That is, they'd have to sell their gil for less RL money than what it's worth on the market, because why buy gil from third parties that could get your account banned when you could sell it on the market legit instead?
This system is, yes, a type of RMT. However, in this case, the trade is only one way: players can only get gil for RL cash, and even then the gil isn't being created. Instead, it's causing players with lots of gil to send it to players with little gil, and boosting the market from increased cash flow. (And as others have pointed out, due to market taxes, it actually takes gil out of the economy!) This system, in essence, is an anti 3rd-party RMT measure, which is what i think most people can agree is the bane of FFXIV. No one likes having Adasdasd and Ddsfsad hogging all the wild boar spots for skins 24/7 and taking away legit players methods of making gil. No one likes Ffdsfsd's party using hacks to claim all the NMs with worthwhile drops. Seeing Sdadfaf and company doing leves all day at cedarwood gets annoying as hell.
This system reduces all of that. It may not eliminate it entirely, but it sure does put a dent in those people's profits, and that is something i think we can all agree on as a good thing. As an added bonus, players that normally couldn't play due to RL circumstances are now able to have a new option to keep enjoying the game with friends. I might even be one of those players paying gil for a subscription myself, if it was affordable enough. As a college student without a job, it's pretty hard for me to make money, so i wind up doing odd jobs to pay for FFXIV. Having a backup option for paying my subscription would mean that if for some reason i can't get any money, then i can still keep playing with my friends. If that means some player with more cash flow IRL gets to benefit by buying stuff he needs in the game that he really doesn't have time for (because you know, some people work 40-80 hours a week, and people with high paying jobs tend to be on the higher end hours worked per week), then that's all for the better.