At the moment it appears that Lutris is designed as an all in one launcher that even handles downloading the runners for you. Whilst I think this is great, it is a little bit limiting if you want some advanced cleverness 
I have custom scripts that I launch for all of my emulators that not only launch the intended game but also does other things such as:
Auto configure .ini files on a rom by rom basis
Launch custom controller configs
Specify fullscreen / windowed mode
etc…
Is it possible (or would it be possible in the future) to use Lutris as a generic launcher by creating your own custom runners that are actually just .sh scripts. Ideally within the runner preferences you can specify the command line to be run (The use of % could be used to expose some of the internal variables):
target_runner.sh %rom %screen %custom
target_runner.sh (your own custom runner used to launch an emulator of your choosing)
%rom (target file to play [could be a rom or an executable])
%screen (fullscreen or windowed)
%custom (custom command line field within the individual game preferences)