Yes everything that you've said about mixers needing to be in a certain gain setting for best sound and least noise is absolutely true and also, bi-amping is overall the best way to run a PA although not the easiest. I use a Mackie 808 for live gigs with a Crown for monitors. Bi-amping isn't really an option with that unit without modding it so although I originally planned to do the mod, the amp works fine as is and I haven't felt the need.
But none of that really addresses the questions he asked in his original post and besides, if you start talking about bi-amping, now you're basically talking about replacing the system. Bi-amping probably doesn't make sense with the type of speakers he's using. Further, his main concern hasn't been sound or getting it loud enough or any of that. All he was wondering is whether the clipping light is a bad thing and the fact is, brief flashes of a clipping light rarely mean anything to worry about since, as you said, the clipping lights are just a general guide and don't neccessarily mean the amp is really clipping. As for blowing speakers ...... the main thing that'll get damaged is a tweeter ..... it's pretty rare to fry a woofer unless you get into hard full time clipping which isn't what he's described. In an ideal world you'd never clip at all but that's rarely the case for people who don't have unlimited budgets for lots of power. I've had maybe 50 different PA's altogether in my life and I've always run them like I've described ...... letting peak indicators flash briefly (as it says is ok to do in virtually every manual out there) or letting peak meters peg occassionally and in 40 years I've never blown a single speaker with the exception of one small horn in a monitor that I used for a bass bottom (understandable) and two Altec 808's (801's?) back in the day and they were known to be very fragile diaphragms.
And I've been in some bands that played extremely loud and we still didn't blow anything
