I don’t know what you’re referring to as “finally” having the Kindle export “fixed” (it works quite fine in v2), but have you considered that maybe it isn’t quite so simple as you think it is? 
This has been discussed a few times in the past. With a small amount of research you would have found that the main problem is that since indexing requires one to know what page a word falls upon, and Scrivener as a simple writing tool lacks a page layout engine, it doesn’t know where words are, hence it cannot build an index. And now that is simple.