I can only go on who my particular Cube 3 behaves. But, Auto Gap, on my machine, seems to leave the print gap too small. So, right after running print gap, I check the height with the included gapping tool. If it's too low, I use the manual gapping option to ensure that my gap is not the cause of a clog.
So, whether you are starting with a new printer, or a newly released cartridge with the updated filament, it might be wise to check your gap before accepting that auto-gap was truly successful.
Remember, my machine was one of the early releases that uses a shim to align the print jet tips. Later machines have a fixed print jet with no user adjustment. It might be that while my print jets are even, they are evenly misplaced and that auto-gap assumes they protrude to a specification that I have altered too far in or out.
In any case, it doesn't hurt to check the gap when auto gap finishes just to be on the safe side.
I am trying to find whether the auto gap applies to the print housing or to a particular print jet tip. Watching it work, it seems to me that it is setting the proper distance for the housing and assumes the tips are protruding a precise distance. I suspect both print jet tips are even; but, may now protrude too low on my particular machine... requiring the manual refinement.