Selection criteria for kyogre raid

I suspect the auto-selection favor defense over attack, and Venusaur has a higher defense stat than exeggutor. So, venusaur might last a little longer, and maybe even have a higher total damage output before fainting. Conversely, if you want to maximize your attack bonus and chances of completing a raid, you might want to burn through more mon, and have a higher overall DPS. In this case, you should select exeggutors.

As was said already, autoselect values tankiness over attack, which is why it chooses Venusaur over Exeggutor and Rhydon and Tyranitar over most things.

What I think explains your lower CP Venusaur being first is that to me it appears like the game ranks charge moves based on their raw DPS, so it absolutely loves Stone Edge, for example. PB has higher DPS as a move than SoB so autoselect likes it more, even though SoB is actually the superior move.