Yeah, there is that to contend with.
I've never used an airbox with my LT's, just an open element filter.
I think the RM500 uses a straight intake boot with the same diameter, but it only works on an 87.
Another option is to get in touch with 500Fanatic and have him build a billet intake boot to your specs, they're pretty sweet.

Aside from that, you can use the stock boot, just keep an eye on it.
If that rubber cracks you'll have air leaks to deal with while you're tuning too.