So currently individual leaderboards can only have the same timing method as the full-game runs. For example in Quake we allow people to submit runs that are Real time if they don't manage to get SS and get an in-game time. Real time is completely useless in ILs. But at the current state you can't opt out of having both RTA and in-game time in the IL boards. (you could leave the real time as blank but it looks like ass)

I asked about this in IRC loooong ago. But I'd like to hear if you stopped working on it/it's coming soon/it's on halt.

This, as well as other timing related things that people have requested for a long time now, has been on halt since all of us have either been working on other things or haven't had time to work on it. Now, I'm hesitant to promise too much as other things might pop up and take precedence, so lets just say that as it stands, there are not a lot of things on the todo list with a higher priority than this.

In the meantime, disabling the 'Show empty time columns' option (which you've already disabled in Quake) might offer some help (it's not a proper solution, but better than nothing). Just like the In-game time column doesn't show up for full-game categories where there are no runs that have an IGT set, the Real time column won't show up for IL's where there are no runs that have RT set.