I personally doubt vacuum has any significant effect on oil flow.

And even if it does, the specifications for flow volumes are given by Yamaha for the stated test conditions.

For example, you check the transmission oil level with the bike level on flat ground.  Leaning it over onto the kickstand is going to give you a different result.  

Yamaha does not say to test the oil pump output with the hose somehow connected to a running engine so even if that does make a difference, you wouldn't do it.  

Getting too technical for me lol. I had some odd ball carb on my ride to work bike once. Must've been my dt250 where the oil line fitting is on the carb. But carb I used didn't have that fitting. Carb had 3 breathers including the bowl tower overflow. So simply plugged the oil line to a breather high in on one side so the oil went in & mixed in the bowl. Never had a problem. Sorry that's getting off the case I know.