I swear, wasn't there an EMG questions board here a few years back? They should make one...
Okay, to the questions.

I'm looking to buy a Jackson KVXMG, which has the EMG 81/85 set and a single volume and tone knob. Now, I'm replacing the 85 with an 60, so would it be possible to keep the single volume and wire both of them to that one, but put separate tone knobs on there? I'm wondering why they'd put a single tone knob on there anyway, because in stock, EMG's come with each their own tone knob.
There are many different ways to wire a guitar. If you can think of it, it can be done.

The way your guitar your considering buying is wired isn't exactly how you think. Neither pickup is actually "wired to" the volume control. The volume control is wired to the output jack and the selector switch. Same with the tone control.

What you'd have to do to get two separate tone knobs is basically this:

The only difference you'd change the value to a 25K pot rather than 500k.

Here's the EMG diagram, but it doesn't show what's actually going on as well. Just tells you what to do (diagram 2):