I've been a hobbyist programmer for five years now, and have a decent understanding of what it's like to work with a decent size codebase. From a number of perspectives, I find it hard to see why Microsoft wouldn't want to switch to the non-Java versions of the game.

1. The codebase is (almost certainly) cleaner. Minecraft's Java version started as a hobby program by Notch, who was just making something because he thought it would be neat to have a world of blocks inspired by Infiniminer and Dwarf Fortress. He did not expect Minecraft to get the traction that it did, and the Java codebase can show for that. As a general rule, typical hobbyist programs are sloppier and harder to work with than typical professional programs of the same scope. If Microsoft were to work with Java version over other versions, they would spend more time working with sloppier code, costing more money, for a version which has worse performance than the other versions.

2. Other versions have a higher performance. In this day and age, people tend to look for games with better graphics and higher performance. Oftentimes on review sites, a section of their rating criteria is about the fidelity of the game's graphics. Why should Microsoft be promoting a game version with worse performance than their, higher performance, versions? Ex. I can render up to 12 chunks on my PC before it gets laggy on Java, but can do up to 48 chunks on the Windows 10 version.

3. The sales are on the Unified/Community edition. According to this graphic, most Minecraft sales can be attributed to console and Windows 10 / mobile versions of the game. Why wouldn't Microsoft want to focus on the game versions that are making sales? It wouldn't make sense to focus on the version that sells the least in all regions (except Asia where it beats Console editions).

Microsoft is logically focusing on other versions of the game because it's easier from a programming perspective, game performance perspective, and sales perspective. They won't listen to the loyalty of the reddit community, because it doesn't make financial sense too. And companies, by nature, have to focus on the money.