The scriptmodule is thought as a "ease of use" / for default setups, if you want to unleash the full potential of Skyscraper use the command line.
Within the scriptmodule you can only alter the (output) gamelist (-g) folder and media folder (-o).
With Use ROM folder (Enabled) (see generate options in the menu) the gamelist location is
/home/pi/RetroPie/roms/<platform> and /home/pi/RetroPie/roms/<platform>/media.
With Use ROM folder (Disabled) the gamelist location is
/home/pi/.emulationstation/gamelists/<platform> and /home/pi/.emulationstation/gamelists/<platform>/media.
The inputFolder is in any case picked up from the config.ini, however, the scriptmodule only uses $romdir which is currently taken from the default RetroPie value (which is /home/pi/RetroPie/roms). See _list_systems_skyscraper() in the scriptmodule skyscraper.sh.
TL;DR: Using a symlink as you did is the right way.