On the "grunt" thing we've never had a need for the art before but ingame it could just be this game's version of male/female scientists,ect.
What about the ambiguous timeline of ORAS Hoenn?
Hoenn's timeline isn't ambiguous. The events of R/S/E/OR/AS take place at the same time as Gen 1, placing them before Looker's introduction in Platinum, so that's noteworthy.
Now, if you mean it's ambiguous because of the Delta Episode Many Worlds Catch-All, then I hate to break it to you, but none of the Pokemon games have a defined place in any one version of the timeline. Any given game could talk place in any universe, either existing or new, since GF opened up that can of worms. That way they can introduce anything they want, and have a perfect excuse to explain away the retcon.
That said, we know that SuMo takes place after X/Y, which means it takes place a while after the events of ORAS. While the exact timeframe is uncertain, X/Y seems to take place at least 7 years after Gen 1/3.
So, in the end, could he have had a run in with the Aether Foundation? Possibly. That, or maybe it is explained by the Sinking S.S. Anne Theory. Honestly, it's tough to tell when we still know so little about the Aether Foundation and their true intentions.