Overworld items are determined by the game's script files, which are largely undocumented.
Keep in mind that each new game increases in complexity, and very few people do heavy lifting with respect to advancing community research & tooling. The scripting engine of gen 3-5 is the same; gen 6+ uses a more complex engine.
If you are unsatisfied with a program's presented feature set, feel free to implement the functionality yourself and submit the patch, or, make your own programs. How the developers choose to spend their free time is up to them, not up to the whims of non-paying (and occasionally entitled) users.