Using a game I run as an example: http://www.speedrun.com/Antichamber

Typically there will be an overall "Any%" for most games, as well as other alternate "any% some restriction" categories. These don't really work as variables because variables can be left blank (which would also be neat, a tickbox to make a certain variable required) and if you're running a different category, you'd want it to show up on a separate list.

For Antichamber, there's the overall Any% which is typical, and there's also Any% No Esc, Any% All Guns, and Any% Jumpless which should all be sub-categories of the main Any%. Any times submitted to these three categories should have their time included on the main Any% list as well, if it is the fastest time they've gotten out of all the Any% categories.

There's certainly some room for improvement on the site end with regards to variables; I think it makes more sense to abstract variables to "optional tags" and "required tags"

Right now, unfortunately category is pretty much coded to mean "Keep this separate from other categories"

I think it would be an improvement to just apply various "tags" to runs and have some of them be required. You could then have "any% (required)", "no esc" and "jumpless" on the same run. The leaderboard listings would then have to be sets of filters applied over all the tags.

It's substantially more complicated than what's currently implemented, but I hope we can work in that direction over time.

Until that happens, why not just simply reject any submitted runs that don't have the variables specified?