Uhh, 3D models are very portable. There's standardized formats that can bake in both the mesh, rigs, and animations — if you need a different format, you just export it to the different format from the source app (Maya, etc) — and yes you could even automate this process with a script to quickly convert thousands of assets. The idea you're suggesting that you have to remake a model from scratch or even re-rig the mesh to get it into a different engine is just bizarre. Like, what do you think happens to the rig and animations in Maya (or whatever app they use to author the assets) when they started working on SwSh? Disappear? No.
No, CPU architecture has nothing to do with models. Again, these are standardized formats -- you write an importer to import 3D assets like you would images, sound files, etc -- you don't reinvent a new 3D asset format every time you make a new engine just like you wouldn't reinvent jpg, png, tga, wav, ogg, mp3, etc.
And for what changes CPU architecture did require (in engine code, mostly), they already had Switch experience with Go P/E — that was supposed to be the transition game.
Maybe they did rebuild the models from scratch, but it would be a creative choice -- it wouldn't be mandated by all these reasons you try to give. And judging by the footage we've seen, I'm still skeptical. Take Gyrados for example -- even the model's topology looks identical. If they rebuilt that model for Switch, why leave in the low poly joints in the whiskers? If they were recreated from scratch, they were recreated to match the old model as close as possible... and I assume Game Freak is smart enough to not waste all that time recreating assets they already have.
(can even see that the part where it starts to curl is a bit squished in both the 3DS model and the Switch model, suggesting they're using the same animations that deform the whiskers the same way --
it'd actually be quite a lot more effort to literally recreate the same model and animations from scratch and have them match up so closely instead of naturally having different proportions, topology, and animations)
Either way, the reasons you provide for why they'd have to recreate or re-rig models is nonsense. If all you claim was true, they would have had to redo all the models and animations for Pokemon Go as well.
Hmm.