Your center speaker is much louder because (a) it's probably got a much higher sensitivity than the paper **** that was in there, and (b) the reduced impedance is allowing it to be driven more easily by the stock headunit.
You've created an artificially enhanced soundstage with a pronounced center bias by making this change. If you like it, great...that's what it's all about. But, your point about imaging without it has some validity, too. The low placement of the 6x9s means that where you/your leg is can have a big impact on what you hear from that speaker and how the system images. Even the crappy stock midbass driver puts out/is crossed over for a good bit of audible and directional midrange sound, because it's essentially a component set with the A-pillar tweeter...it was one of my original criticisms of the system. Because you went back with a 3way in that location, it's probably producing even more midrange that can be affected.
But, over-emphasizing the center channel is not the preferred outcome for true stereo imaging. You are going far beyond even the DSP profile for a center channel-enhanced soundstage that was engineered for the factory setup. I was messing around in my stock 2018 yesterday with the DSP on, and I put a large book over the center channel at medium-high volume...almost totally inaudible difference. The center, as designed, just doesn't do/add much but fill/presence for the DSP. Again, if you like the very forward soundstage your setup has created, keep it. Otherwise, I'd follow the advice of the pros above.