Which is literally not usable for my work.
Because? Whats the reason to give them the same material if you don't want the objects in the same TextureSet?
Is there a way to work with them in substance painter as objects not as material IDs texture sets??
You can either split you object into separate TextureSets using material assignments, or UDIMs. You can't hide objects independently from TextureSets, if thats what you are asking.