Which three.js version are you using?
Three.js has supported 2 UV sets for a while, but had major restrictions on how they could be used. You couldn’t pick and choose which texture used which UVs. Beginning in r151 you are still limited to 2 UVs, but you can assign any texture to either of them. Beginning in r152 three.js supports up to 4 UVs, and you can still assign any texture to any of them.
I’m not sure which releases of Drei or three-stdlib correspond to those three.js releases, though. Blender and Blender’s glTF exporter should have no trouble with any of this.