https://www.pokemon.co.jp/special/hgss/character/rocket01.html
I feel that this link may help us on the guessing on this Kyogre/Groudon Subplot. If you look at the top, there is the section with Team Rocket (which the link leads to). But if you continue to look, you will noticed there are three "Coming Soon" tabs. I believe these may just be Team Magma, Team Aqua, and Team Galactic.
The Team Magma and Team Aqua could be in this game for this little subplot, and the reason I think Team Galactic might be is because of the Arceus event (that I highly doubt they'd be there for). This is just speculation though. xD
So I think there might just be a separate little storyline for this whole thing and they might try to avoid the roaming legendary thing from Emerald.