You DO know what a retcon is, right?
Regarding Emeralda, she's not a nanomachine colony. She's a biotechnological construct based on nanites. Big difference, as it means she's part organic. Remember, Kim and Elly made her with THEIR genetic code. She's pretty much their daughter from a biological POV. The nanites just allow her to decompose and reassemble herself, as well as alter her structure, but the organic part is still there.
So yes, it'd be considerably LESS messy to use her, since unlike KOS MOS, all her abilities are enabled by her nanites, and if Emeralda somehow created a spring, it'd make sense for some of her nanites to have been left over there.
Seeing how she lasted 1,200 or so years in Zeboim without them running out of energy, and seeing how Jusenkyou looks like it'd be full of 'ether' (assuming that is even what powers her up, which I doubt - she was still active when the other Gears shut down, BTW, which is proof she either has a different power sources or is more organic than nanomachine - she'd otherwise have died on the spot), having a 'spring of drowned Emeralda' is very, very feasible, and could account for a Ranma with actual nanomachines inside him.
Meanwhile, KOS MOS is for the vast majority an artificial being, so she'll cause messy things when you take into account Third Armament.
And finally, the nanomachines would actually make the transition from normal to cursed less traumatic than being full machine or anything like it. Remember, nanites replicate themselves, and even after ranma reverts, teh ones that were replicated won't disappear, as they aren't Jusenkyo-made, so he'd eventually be a biotechnological lifeform regardless of if he's in cursed form or not.