Thanks, I read the article that is linked within the Emma report, about the candidate's description of the event.
When he candidates "as a woman", he is asked by the board members about how far he transitioned, and how he feels, and replies that this is not about his feelings. That according to their own statute, declaring himself a woman is enough to candidate for the women's spot.
They must have been so conflicted, being called out like that and having it highlighted how easy it is to "misuse" this rule. That's why they had to let him on the ballot, otherwise their own construct would have fallen down and they would have been out of the official party guidelines. It's clear they weren't really believing him, either, but too scared to call Emperor's new clothes.
The latter decision by the parties' own court is indeed completely absurd. But in fact it could have contributed to the parliament bill - they just moved the self-declaration to another sphere: If the party should go by GRC-alike declaration in the population register, then the GRC must be easy to obtain - and they moved it to Germany's administrative sphere.
In that sense, the Greens went against their own rules with the Markus/Tessa Ganserer-example, as @Delphin said.