Interestingly, there's a flashback scene in the manga, set not long before the present day, in which Cynthia is accompanied by her Garchomp while it's still a Gabite. Reminded me of this.
An NPC in Fortree says that he met Steven and that the team he was using "weren't just strong, they were trained to terrifying extremes!" That kind of implies that he was using his Champion-level team, though I think we're meant to assume that the individuals he uses at the Space Centre are the same as the ones he uses later.
But levels in the games are kind of abstract imo, so it can be rationalised with that in mind. Reference how Eagun's Pikachu - explicitly the same one - goes from being level 50 in Colosseum to being level 12 five years later in XD. I've always thought that levels (regardless of how they work for the player) aren't a permanent state - a level 80 Pokemon which isn't being used might start to get out of shape and lose the experience it previously accrued, dropping to a lower level after a period of inactivity. The only reason this doesn't happen to the player's Pokemon is for gameplay reasons (imagine going on holiday for a couple of weeks and switching on your DS to find your level 100 starter was at level 40 again...)
Emerald establishes that Steven, despite being a powerful trainer, rarely battles and spends more time looking for rocks. So once the player becomes Champion and Steven decides they're worth battling, he begins a more rigorous training regime (as do all the Gym Leaders, canonically) to get his team to the level where they're ready to take you on. The Metang he was raising might be the same one he uses in the Meteor Falls battle as a Metagross. But that's not to say it's not his first Metagross. He says it's his favourite Pokemon, so he'd definitely train multiple individuals - he has numerous Beldum and Metang in the manga, and of course trades you a Beldum in HGSS.
As for the Beldum he leaves you, he might breed them but alternatively I always assumed he'd just found a place in Hoenn where they could be caught that the player doesn't know about.