Just use a bigger tray
Grouping doesn't mean they have to be bundled, you just need to run the whole group together in a single tray (or parallel trays are OK too, I believe). If you can leave a cable diameter between the 500kcmil cables, you don't need to derate at all. I've often seen them tie-wrap cables to the trays to maintain spacing. Looks cheap with all the tie-wraps (IMHO), but very clean, and is very effective at maintaining spacing.
I really don't see why NEC would specifically disapply 310.15(B)(2) though, it doesn't make sense, and 65% is a HARSH derating. Ask your AHJ, they may be lenient about minimum cable space to avoid derating- I know I sure am on cable spacing in venetilated trays.
Alas, I won't have to worry about this anymore- as of 2008, 708.10(C) specifically prohibits it for my sites, even when the EMI environment will allow open tray. All RMC from now on, I suppose. Maybe the occassionally SCH80 duct bank...