Will the Retaliator have variants in addition to the modules or does the modular system replace variants?

This will depend on the ship. Some will continue to have variants while some will have a single base with modular portions (think of how real world aircraft might have the ability to be retrofitted for different roles, while others might have several different types manufactured depending on missions.) As a rule of thumb, military ships are more likely to have traditional variants than civilian ones.

We do not currently plan additional Retaliator variants, although they're possible. It's likely the UEE has built several different hulls over the year! (Similar to how there's a B-17D, E, F, G and so on with various improvements/changes.)