Allisons are easily kept cool with a decent trans cooler, just like any other transmission. They don't flare unless the fluid is beyond burnt. The Allison is an EXCELLENT transmission.... once it's built. In the stock form I couldn't care less for it. I have a suncoast trans in my 03 dmax that has 50k miles on it at 500+ rwhp, towing or not it doesn't get a break. Always over 500. It hasn't given me any issues whatsoever since built. They're fairly easy transmissions to swap because they are learning transmissions. I still don't have tcm tuning even with compounds on the truck. Factory transmission tune. When towing I've never seen over 185 degrees with my setup.
However, the STOCK torqshift in my 6.0 sees 600 hp daily, and while it's not happy about it, is holding up great. I know how to treat it, I know what pisses it off, and I go around it. No way in hell would I trade a stock 5R for a stock Allison.
Edit: the stock Allison shafts are good for ~1200 rwhp, they are certainly not weak. They're twice the size of a ford/dodge input shaft. They will NOT limp at stock power. They really only limp when slipped. If the truck is at stock power the Allison will last forever. And actually, a 6 speed Allison would handle the power of a max effort race tune in a 6.0 without hurting it ever, simply cause a 6.0 puts down far less power than a dmax does on just tunes. They just don't have the same fueling capabilities.