Re: Interesting ......
I think Minecraft, despite running on Java, doesn't even register on Oracle's radar as a 'killer app' that drives people to install Java. Microsoft doesn't want distribution of Minecraft to be hampered by problems that users have with installing Java from a third party, and Oracle probably would prefer not to have to support users having problems with the backend of a mere *computer game*. So bundling a dedicated JRE, that one would expect to be streamlined, tested, and optimized for Minecraft, is really a win-win for both companies and hopefully end users as well.
As re: modding, I think that for better or worse that is really up to Microsoft, and not predicated either way by custom Java. Make it open, people will figure it out and have fun; lock it down, fewer people will figure it out, the community will be a bit less fun.