Someone asked a while back where a good place to do runups is when there is not one designated. I have also come accross this once or twice. The first time it led me to doing runups in a twin on the roll which took up a lot of effort on the taxi and I'm sure my instructors wouldnt have been happy. Bit dodgy of me.
Runups before each flight is -as I understand- in my ops manual and I would prefer to do it when not required by ops manuals cos things do get missed when you leave it to other people.
I find into wind helps at GAAPS because it makes ur aircraft's position and entry/exit in the bay predictable to other aircraft and since the aircraft will all point the same way, you won't be prop washing others.
Personally I have few problems with checks on the run, good practice for larger operators. I follow their procedures such as pausing checks when crossing runways and 'clear left/right' approaching taxiways. Of course all subject to workload, safety first and speed/efficiency second etc etc.