The negatives that I see is that you are needlessly burning fuses for relatively little to no payoff. Burning fuses inherently carries no advantages because there is zero evidence Nintendo has banned people for mismatched fuse counts. The only possible upside is because people do not want to boot emuMMC online. Now if Stock emuMMC weren't broken, this is where the conversation would end. But I can see where some people are coming from. On the opposite side, ask anyone in the ReSwitched Discord and nearly all (if not everyone) is using Atmosphere online 24/7 without a ban. Of course they aren't doing anything super shady like piracy or cheating but, at least from their data, booting CFW is not enough to warrant a ban (or just Atmosphere). Thereby booting emuMMC would basically carry the same risk.
At the end of the day, its just as you said, there is no way universal way to use the Switch. Since we already have an exploit that can never be patched, there is no right or wrong way to hack the console. Personally, I want full control of my console and that applies to fuses. Some people have thought it is partially illegal and while I think its bogus, we should have control over that much of our consoles.