Can I still control the perceived sound quality when FIRmaker optimization is applied?

Yes, absolutely! You might even notice that your applied EQ will produce more consistent results throughout the whole venue than you have been used to before.

The reason for this is simple. FIRmaker is a set of numerical algorithms able to optimize your system's performance. "Optimization", in this sense and within the parameters you set, attempts to tune the system for...

an even frequency response throughout all audience areas of the venue
an homogeneous coverage over all audience areas of the venue
an evenly high SPL at every seat in your venue.

On top of that you can do all tuning as desired to add "sound" and "spice". — You can rest assured that your personal flavor will be heard throughout the house with the same tonal quality as at the mixing desk.