3 attack stat is insignificant enough that A-Exeggutor and normal will have almost the exact same cycle DPS provided they reach the same Bullet Seed breakpoint. Alolan then gets a better time to win because it has to go through a lot fewer death animations and may skip rejoins that normal Eggy would have to go through.
Kyogre counter update errors?
I'm not sure the currently updated page is correct. For one, the numbers for old counters are significantly different from what they were pre-update (e.g. ~2 TDO and 13 DPS for Raikou before, now higher for both). Additionally, it says that Alolan Exeggutor has higher DPS than regular Exeggutor, which doesn't make sense since they have the same moveset and Exeggutor's attack stat is higher.
Answers
That makes sense, but I'm talking specifically about the page on this site, not Pokebattler, where it lists TDO and DPS rankings. DPS-wise with grass/grass, Alolan Eggy shouldn't have better DPS (even if it's only a marginal reduction). That also doesn't explain the discrepancies between the old page and the new page for old counters, unless Kyogre got a nerf or moveset change.
Kyogre's Raid Counter guide data was updated with GoBattleSim data instead of Pokebattler. This is the reason for the shift in numbers.
As for Alolan Exeggutor having more DPS, GoBattleSim factors time switching Pokemon into its calculations. Since Alolan Exegg doesn't switch out as often it does more damage.