An A380 set up as a cattle car should take longer than norm.
An A380 with 60 suites in it (or whatever) should take shorter than norm.
With that said, assume turn times are based on the standard setup.... more pax, more time.
I don't see how this is possible within the UI given that the specific AC is not known when designing the route, but maybe it can be done on the backend? (similar to payload restrictions when an AC has many range variants available)
When calculating actual delay % for a given flight, consider the # of pax the AC is designed to carry in its current config, and adjust the delay % up or down accordingly. And the delay % shown on the route design screen can be either worst-case scenario, or can be using the factory default config (with a note explaining that).