One of my guitar amps (victory Duchess) has defeatable EQ, and I really dig it. EQ is there if you want it, but when removed from the signal chain, it's a different sound, and definitely changes the response.
In fact, I also have boutique tube amp with the same option, it's called "Pure", and it removes the EQ section all together. Like for you, it's a different sound (it doesn't sound like when all is EQ knobs are at noon, or 0 or max, and it's louder). That because the EQ section is passive.
I think what OP has in mind is different: in the case of the GR Bass amps, with active boost/cut EQ, I think the option to defeat the EQ section sounds like when all EQ knobs are at noon.