FSLTL does not clear GA aircraft off the ground; setting the sim ground aircraft to 0 ( as suggested by the FSLTL team) does that.
I use FSLTL and still keep ground aircraft and AI offline traffic at around 8%. This adds GA aircraft to the skies and ground and still allows FSLTL to function, albeit at a increased computing cost.
As an alternate, you can set the AI offline traffic to 10-15% and use the offline GA traffic mod. This has less of a frame rate hit but it only has 5 different aircraft and seems a bit repetitive.
Hopefully, Aerosoft or other 3rd parties will create a traffic program that addresses both.