Most Super Tens are more susceptible to stalling this way when new. My '12 was like that, but after a few thousand miles it went away. No need for a flash, just ride the bike. The mentioned things to do/check are all good and not difficult. We set our bikes up to suit our tastes and needs.
The '15 that I bought used with low miles never exhibited the stalling. Not because it was a Gen II or anything done to it, just because it was already broken in a bit.
Wroth a mention is for riders coming to the S10 as their first experience with Throttle by wire, there is an adjustment period. Throttle control has to be managed a bit more closely/finely than with a non TBW EFI bike. And if someone comes strait from carb bikes to TBW, they usually hate it and have a more difficult time adjusting.
My preference is for very little throttle free play. Less than Yamaha specs in the service manual. And I rode my '12 in T mode for the first 600 miles, changed the oil and put it in S and never used T again. If it accidently got into T mode, I'd be instantly wondering WTF after the first shift, then flick it back into S mode and all was well again. T feels so lazy once you're used to the throttle movement of S mode.