He codes with what he knows to get a prototype. I bet he'll get a team of smart guys involved once it's time to get the game running on other platforms.
Of course, it'd be better in the long run to stay up to date and eliminate that extra work, but sometimes it helps to build it first to see if it'll even get to the refinement phase.
I don't think Minecraft ever got updated to using the correct APIs; I doubt this will either.
Minecraft is still in active development. It may yet (if it isn't already).
I'm quite sure that such a major change in architecture will be completely infeasible by now. The whole renderer would have to be rewritten from scratch, and given how the Minecraft codebase appears to be a complete mess architecture-wise, the changes would probably reverberate everywhere.
It's a real shame that when he decided to completely rewrite the Minecraft engine (which he finished but regretted), he didn't switch to using Modern OpenGL.
Actually using the deprecated immediate mode is the only possible way to get compatibility with the indie game user base. Minecraft only requires OpenGL 1.1 and I think it's a key element to keep players happy.
Multiple rendering path are of course possible but require much more work.
Which ones?
Immediate mode, fixed pipeline. glBegin(), glVertex4f(), etc.