I thought everyone knew Snake learned who The Boss was, along with CQC in MGS3 and MPO. Both of which are really just VR simulations that Solid Snake went through to learn about the Patriots and Big Boss. This was set up by Col. Cambell, and constructed from the memories extracted from the cells in Big Boss' remains, eye witness accounts, and the files on the mission kept by the Patriots (that Otacon had retrieved from hacking Arsenal Gear). When Snake failed, or did something wildly inconsistent with the mission parameters outlined from what they knew definitely happened during the mission, the Colonel would reset the machine, while scolding Snake that his actions would create a time paradox had it been real.
Seriously though, I have no idea if they plan on connecting The Boss to Solid Snake, but I wouldn't discount any theory (except maybe the one I just mentioned or time travel). Especially since this is a series that contains: a transplanted arm that can take over its host body, vampires, someone who can shoot bees from their mouth, and a women lucky enough to divert missiles fired at her, excetera. The possibilites for how they could handle it or those other mysteries are endless considering how crazy the plot already is.