Yeah, but he also has the optic camo in the opening. >_>
I've never interpreted most of the little references as anything more than just references. Sly winks to the people who have played them rather than solid narrative connections and inferrences. Either ending you get conveys it's own unique information and perspectives (like the fact that meryl was cambell's daughter), and I'm sure they were intended to be equally valid. Basically, you can only get the complete story by witnessing both endings. It's a form of narrative progression that is unique to the medium.
Like that 'other' big PSX game that was never expected to become so prolific - biohazard/RE, where 3 of 4 main character survive depending on who you're playing as, and rebecca or barry are either never introduced, or presumed missing from the start. Their fates are left up to pure inference that they both survived, but their circumstances are simultaneously true depending on which game/event is referencing it.
I'm only saying this as someone who believes video game narratives shouldn't always be percieved as 100% linear where a single canon is always necessary, but as a malleable, mutable thing that differs from person to person and mgs2 (like biohazard 2) treated it as such. The longer each series progressed they stopped being able to avoid making clear connections to their projenitors.
Regardless, mgs4 made it all irrelevant and any conjecture is now moot, which means I'm babbling for no reason.
Thankfully I can keep on trying to forget that game ever existed.