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.
https://github.com/kugelrund/LiveSplit.Quake (Download from the "releases" tab. Read the readme first tho) edit: The easiest way to install this now is to just choose Quake as your game in splits editor and click the "Activate" button.
Auto split / in-game timer for Quake. By based SphereMJ. You need the latest JoeQuake-gl and qdqstats18 for it to work. Get them here: http://joequake.runecentral.com/downloads.html http://quake.speeddemosarchive.com/quake/downloads.html
Also ask here if you have problems using it.