Yes absolutely - but i never suggested that it was purely time based.
In the BB Game Analyzer (178926.1) built by moutlinho (70514) - It is stated that the shot quality can be measured somewhat by the time during the 24-shot clock period a team takes a shot.
the idea being that, shot quality is a measure of your individual and team's offensive tactics and player abilities - as you said, inside shot, passing etc.
So for eg: If your team is consistently taking shots inside the last 5 seconds of the 24 second time allocation, it means opposition team is playing awesome defense + you are playing a slow offense + your players are crap + you have aweful offensive flow etc etc etc.
Now - taking the way it currently works as a real life example. If there are 12 seconds left in the game, the shot clock starts at 24. when the game clock hits 4 seconds, shot clock is at 16 and if my team's offense run for that run is good, i might get a shot up. It will be measured as a shot taken at 16 seconds - which according to moutlinho's rules - is a shot above 5 seconds which to quote moultinho's spreadsheet - "are expected to have more possibility of going in compared to the shots taken under 5 seconds."
So if you change the shot clock to match game clock, in that example above, my shot will be taken at 4 seconds, which, is classified as a lesser-quality shot, which, either in terms of the game engine, or in terms of moultinho's spreadsheet, i really dont want. :)
OK, I understand what you are saying now...
Another solution is just to use the min(ShotClock, GameClock) at their code for defining the shot to be taken.
In other words, I agree with your observation, and suggests to open a new Bug thread about that, but I'm not sure which solution is to be chossen.