The problem is that if you drop all the EQ bands equally, it's no longer starting out flat. Its base output is then already bumpy at that point.

When you do the RTA, your goal will not be to remove dips in the spectrum, it will be to remove peaks. So if you work with the mentality from the start that you're cutting rather than boosting, you'll be OK.

As far as "never using bass/treble/loudess", those things do have their place, and they are much easier to adjust quickly than EQ settings are. Ideally, you would tweak the EQ so that it sounds great with no bass/treble/loudness, and then only occasionally alter those values for special situations, such as you're playing a particularly bassy album and you need to dial it back a bit, or you have a friend in the car who likes more bass than you do, etc.

I find that when I have passengers in my car, I need to increase the bass and loudness a bit. Dunno why, something about the acoustics.