It would be nice to be able to have the ability to have certain categories be IGT and others be RTA

I do believe default sorting for specific categories is planned. As for restricting entries to either IGT or RTA, for the time being you can just state in the rules to only use one or the other.

In my opinion, every category should allow realtime as an entry, but the default sorting can be different.

Relatedly I'd love to have some categories have load time subtraction, but others not.

For Zelda 2 there's only a few categories (the FDS runs) where subtracting load times even makes sense, and for those it's mandatory for the board to work out.

I want this as well because for Ninety Nine Nights full game runs we use RTA. However for ILs we use IGT, is it possible to have only this option for ILs?

@skaleks: You can just put in the rules that IGT is used. RTA won't show up on IL board unless they submit the time as an RTA, which you can change. 

~ Token