orso you have 2 options
1. go back later and delete everything you didnt want automated
2. press stop everytime you want to change something and have to start recoring the sequence and other changes you DO want recorded all over again
3. Ignore the fact that track 3 is too loud while you're recording your arrangement and filter sweep. After you've recorded all the parts you want, go turn down track 3.
I'm not trying to be facetious here. I just don't understand the problem, I guess. There have been a couple of times where I have been recording a guitar part or something and I've turned some other knob and had to go back and delete the automation I didn't mean to create, but that didn't bug me too much.
And it's way better than having to remember what exactly you want to arm for recording. Plus, the way it is currently enables you to record something unplanned you do if you have a brainflash or something. It captures good accidents as well as bad, I guess is what I am saying.