I was about to comment to say this is the source of the confusion. The Java based one is the original. Microsoft doesn't have the best history with Java, so my best guess is that eventually Bedrock may indeed replace the original in constant development, but it doesn't appear to be too soon. It doesn't hurt to just invest some time into the Java edition of Minecraft until the Windows 10 catches up with the new mod system.

The Raspberry Pi has a minimalist rendition of Minecraft that let's you script it with Python. Just downloading (or getting n00bs) the official Rapsberry Pi distro Raspbian includes Minecraft with it.