My understanding is that the most flexible of the MOBI types is the "triple" flavor that's produced by the KindleGen program, which I don't think Amazon continues to promote. Inside that MOBI container is 1) the ancient Mobipocket format, 2) one of the newer AZW formats, and 3) the original EPUB that was fed to KindleGen. When you run kindlegen.exe you can give it the flag/option -dont_append_source and then it won't include the original EPUB. Ancient Kindles will automatically use the ancient Mobipocket format while the newer Kindles will automatically use the AZW format.
Google can provide the amazon download page for KindleGen.
On Windows KindleGen is a DOS command; here's the .bat file I use to run it:
Code:
@echo off
for %%i in (*.epub) do start kindlegen kindlegen.exe -c2 -gif -dont_append_source "%%i"
rem pause