I am not a leet hax0r :(
I admire it more as an accomplishment than I enjoy it as a game, although I do enjoy it. The fact that a team of volunteers could achieve a project of that scope and quality - even with its flaws - is very inspiring. Yet it seems to attract an unreasonable level of hate and vitriol from some portions of the Valve/Half Life fan community, which I find baffling. When a team spends ten years making a free game for strangers to enjoy, it seems churlish and petty to flame them for making design decisions you disagree with, or for being insufficiently slavish in copying the original game. It's represents the ugliest form of entitlement that sometimes rears its head in gaming communities.
The arrangement around the retail version seems rather complicated. As I understand it, long ago, Valve agreed to let the project go ahead so long as they didn't have "Half Life" in the title, hence it became "Black Mesa: Source". A long, long time later, they finally released the project, sans Xen, which they said would come along later. They then set to work on finishing Xen, but beforehand decided to port the whole project to the newer 2013 version of the Steam SDK.
Contemporaneously, they were one of the first projects that was green-lit on Steam, and thereafter reached a proper legal agreement with Valve which lets them sell the game, and also gives them complete access to the Source engine, the same as a commercial licensee would have. In fact, they were required to port the project to this newer version of Source in order to distribute via Steam, whether they sold it or not.
So now they're in the middle of completing two porting efforts: The first to the 2013 Source SDK, which will be released as another free, standalone download like the first release. The second to an undisclosed newer version of the Source engine, which will be released as the retail edition on Steam, and which will have various additional features and enhancements above and beyond the free version.
It sounds like neither of these versions may have Xen, which is still planned but will arrive further down the road. My guess is that they want to get a commercial release onto Steam, then use the revenue from that to reward the team and maybe fund some of them to work full time on Xen and other enhancements, but that's just my speculation. Like I said, it's complicated.