Of all places to learn moderation, my Mesa Boogie Mk III with Simul-Class and EQ taught me to nudge the knobs if I didn't want to end up tweaking all of them!!!! That was a LONG time ago and a lesson I butted heads with repeatedly.
Not just tone either, much like your observations above. The gain knobs were all very interactive and they also affected EQ. Most of the time I shut the 5 band graphic EQ off, just more ways to mess up the tone for me at that point.
Not sure what I would do with that amp now, probably sell it to somebody who wants to fiddle with it!
Recently I started working on getting a bass tone I like going in. Same thing, a nudge can go a long way. I've done it with the controls on Presonus Eureka, with the tone control (passive) on the bass combined with an EMG BTC that I mounted in a project box and now with Tech 21 Bass and Para Driver DI boxes. You're right, it's easy to think "this sounds really cool" and then playback from the recording has you dialing things back because it ain't that pretty at all. For what I like I find the Drive knob and the Blend knob on the Sansamp stuff to be wonderful, until it isn't. A little goes a LONG way.
We fixed an minor tonal annoyance yesterday on the vocals I was tracking just by moving the mic back about 3" and having the singer raise her chin up a little when she was going to get loud. Really smoothed things out.
I've very aware that it can't always be done but often you can solve these issues at the source before committing. It's taking more time as I learn what works but I am hoping it will save time in the long run when there are fewer things that need adjusted later.