After seeing opening sequence few times I can't, but feel during development they must have axed quite a bit out of introduction to the world before dropping you to first planet. Giving little bit narrative disconnect that our character basically gets kidnapped by wanted criminal and instantly tasked by said criminal with random task to get some drugs. You as character have zero reason to trust anything he says or do his bidding yet you just... do? Also game just assumes you (character) are as anti-corporation as Welles is without giving you option to challenge him at all during opening sequence.
Seems such huge missed opportunity to start game by actually fleshing out world right off the bat, introducing Welles.. well.. at all and letting player stretch those "choices matter" legs by letting player actually interact and do decisions with Welles.
They've specifically said that you can turn around and betray Welles for the bounty within the first few hours of the game, if you want to. As for the opening sequence as shown... I don't really have any issue with how it plays out? Like, I don't see where your character would've even had the opportunity to challenge Welles - you've barely woken up, and are clearly still extremely disoriented, before he jettisons you from the ship - and you don't have to do anything he asks you to do. Now, they could've rewritten the scenario to provide the opportunity to actually talk with him, as you say, but I really disagree with your assertion that the game assumes you share his perspective. The game very deliberately does nothing of the sort.
(Also I think it's worth pointing out that he doesn't so much 'kidnap' you as rescue you from being left for dead in a freezer for the rest of time—a fate that you were condemned to by the very government that branded him a 'wanted criminal'. That's not to say that there aren't any valid roleplay reasons for your character to be dubious of Welles, of course, but the perspective of his actions you've presented is just that: one specific perspective, that plenty of players and characters won't share.)