I wouldnt think u would have to run it bone dry. If ur filling up with e85 less than a gallon left should be ok. If you run them bone dry they can pick up crap from the bottom of tank
Your pumps will be fine doing that, if you have the socks on the bottom of the pumps you don't have to worry about what's on the bottom of the tank. Anything big enough to hurt the pumps isn't getting through that sock
I personally would not run the pumps dry. The fuel in the tank helps cool the pump, running them dry and hot then filling with cold fuel could possibly kill the pump.
If the pump is picking up fuel the fuel is cooling the pump. Doesn't matter if the pump is submerged on not. OP, do not let the pumps cavitate and you'll be fine.
An in tank pump should be submersed at all times. Yes, if the pump is picking up fuel will help cool it but without the pump being submersed, you could decrease the lifespan of the pump.