Sure it's separate. That outdoors area is substantial and a completely different environment from the inside of a spaceship. If you were to lump them into one, it would be departing too far from the usual meaning of the word 'environment' and you'd basically just be counting levels except ignoring re-use.

However, by the same rationale there are further distinctions to make. The natural outside area of SC is separate from the facilities. The snowy part of AOTCR is separate from the indoor areas. The swamp area of 343 GS is separate from the facility. The outdoor part of Keyes is separate from the ship (though I suppose you might consider it the same sort of environment as the outdoor part of T&R). This takes the total to 12 already.

What about level 2 though? If we ignore the towers as being minor places in terms of area (even the one having an underground zone), that still leaves the tunnel complex. That's sizeable and very different from outdoors, so really ought to count separately, taking us to 13.

Obviously there's also the issue of how different two artificial areas or two natural areas need to be to count as separate environments. But even if we take a conservative view of that, there's one special case we might consider. The escape drive area in The Maw is a very different environment from the rest of the ship, and I'd say that's worth counting separately, taking us to 14.

Of course, if you go along with all this, your totals for the other games may need revising.