FLEX batting

[JefferMC]

I had this happen on my DD's middle school team while I was scoring. The Flex saw her name in the #10 slot on the dugout lineup and didn't realize that she wasn't supposed to bat (I think once the coaches understand DP/Flex, that they out to spend at least 10 minutes explaining it to the players). Anyway, she was late getting out to the on-deck circle, so by the time I saw what she was doing and got the coach's attention in the 3B coaches box to tell her that her flex was batting, she was next to the plate and a pitch was on the way which was hit and the batter was out.

The other team's scorekeeper apparently didn't understand what had happened.

My understanding that the batter would be out as soon as detected after taking a pitch but before her turn at bat is resolved. What would happen if she hits fairly and gets on base I'm still muddy on. And/or any additional penalties on the batter or coach (ejection?)