PKHeX only fixes some minor issues when you view the Pokemon. But you can not use the Batch Editor for that. The Valid ad Legal properties are readonly, you can not modify them.
If you want to auto-legalize multiple Pokemon you should use ALM https://github.com/architdate/PKHeX-Plugins/releases/latest
What exactly does not work?
You can get the latest automatic build artifact from the azure pipelines. Works fine for me on the latest PKHeX (230925). https://dev.azure.com/architdate/architdate/_build/results?buildId=937&view=artifacts&pathAsName=false&type=publishedArtifacts
Well, you could turn on HaX mode in PKHeX to give a Pokemon the GS Ball, but that won't work.
Having the GS Ball alone is not enough. There are also 2 event flags that have to be set. For that you have to edit your save.
That's because the Pidove was never available like this. These wondercards were never meant to be accessible by anyone, they were used for debugging by GF.
You shouldn't expect anything from the Unreleased/Beta PKM category to be legal. Some might be, but only because they match another Pokemon that was actually available.
You shouldn't open the .bat in PKHeX. If you double click the .bat PKHeX should open in HaX mode.
This guide is a bit out of date. Nowadays you could as well just set ForceHaXOnLauch in the startup settings.