I have an Ender 3 and Prusa MK3S using MK8 and E3D V6 nozzles respectively.
I've read some difference between these two nozzles in question "E3D V6 nozzle vs MK8 nozzle, first layer adhesion".
Can I use an MK8 nozzle in the v6 heater block and vice versa? I know both have same M6 thread but what tolerance do they follow?
To be successful you would need to ensure that the geometry of the two nozzles are compatible. It is not just the external thread. It includes thread length, internal diameter of the nozzle, whether the hot-end is configured for a PTFE liner, or is an all-metal hot-end, how the back end of the nozzle couples back to the heat-break, how the internal geometry of the nozzle sits in relation to the heater block etc.
The original designs that spawned many of the clones were usually highly researched and sophisticated holistic balances of thermal and mechanical properties designed to prevent clogging with the widest range of filaments within the design spec of the hot end.
Randomly swapping parts could alter that balance and cause all sorts of printing problems - including leaks, burned filament within the nozzle, clogging, oozing, poor retraction control, poor thermal control etc.
But, if the geometries of the two nozzles are close enough, you might be ok...
