I use instance variables in my rooms to set up quests and scripted events -- does the plugin offer a way to store and access those variables?

As per doc, you let it know how you want your variables and instance creation code to be processed; since writing the doc, I also released this thing, which can handle variable assignments and simple logic.

In terms of file format, instance variables from JSON are combined into snippets of code assigning them, like so:

num = 1;
str = "hi";