Scrimmage Kick, kicked out of K's end zone

[With_Two_Flakes]

As it happens, since the foul was in the EZ then the result is the same whether the penalty is accepted or not - Safety.
But you flag it anyway as it looks odd not to flag it. I train my guys to keep it simple and follow their routine. In this case - see the foul, take a second and replay it in your head, decide "Yes thats a foul", flag it and keep officiating. Don't over-analyse and start thinking about the enforcement while you are still officiating.
I use the same philosophy for bagging fumbles - bag them all and keep officiating, worry about whether you actually need that spot later on.

What if the foul had been on the 1 yd line? I have seen officials over here in the UK (where we play NCAA rules and illegal kicking also caries a loss of down) who don't flag it, just go with the safety and only later do they realise that maybe B would prefer to forgo the safety, take the penalty and get a 1st and goal.