Rather time without loads. This is still RTA so you don't have to single segment the game.

Go into the autosplitter settings and check "Pause game time while loading and during unit-end screens."

PS: Don't compare to best segments, obviously. HEH

The better way to do this is to keep all timing methods in the layout at "Current Timing Method" and change the current timing method instead by right clicking on LiveSplit -> compare against -> Game Time. That way you can switch back and forth between RTA and loadless time a lot more easily.