TimeLapse is capturing "real" 4K video mode on iPhone 6s.
It's capturing at 4K+. Apple's definition of 4K video is 3840x2160 with a 16:9 aspect ratio. On iPhone 6, TimeLapse uses a much higher resolution of 4032x3024 with a 4:3 aspect ratio (the camera's max available resolution).
In summary, as is, TimeLapse is capturing at the best available resolution. Better than Apple's built in camera app.
The one remaining issue is that Apple's photo library doesn't support 4K+ videos and they cannot be exported there. Though, you can export the videos to Dropbox, Box, etc.