The bottom line is, if you are using a modeler to emulate an amp you need to provide a flat frequency response in the amp it is driving or you are going to get some cut and boosted frequencies that just don’t sound right.
There are still many variables that are not taken into consideration such as the tone shaping circuits following the tone stack in your amp, phase inverter, output tubes, transformer, speaker etc. But the tone controls are your interface and provide you with 80% of what you need. Setting your amp flat first will give you a known starting position to twiddle from. And you should be able to get the tone you want much more quickly from a known starting position. Another thing to remember about modelers- they are not meant to give you the exact sound of the different amps out there- it is impossible to do that. You can’t make a Bassman sound exactly like an AC30 with Alnico Blues. But they do give you a lot of versatility and give you sounds that are in the ballpark. Stomp boxes are great too. All of these things have their place. Rock on!