Any tier of perk can applied to and factory, however it will be capped at the maximum allowed.
eg. Tier I factory with a Tier II perk will work but gui will show Tier I.

Gui should indicate this cap is being applied as it is currently confusing as to why the Tier II is not working correctly.

When the factory is formed then we lose the information regarding what the original perk tier was.
One option would just be to set a boolean in the FormedSetup if any capping is taking place.
Then the gui can do something appropriate with the general "capping=true" value and highlight the perks in general - eg. tooltip for each perk could say "capped at Factory Tier 1 level".