this is an interesting point you bring up. TT did in fact have “at the end of the match” as part of the scoring definitions for both cubes in the goal areas and cubes in towers. Yet, there was obviously no question that they also counted during auton, because like you say, it would have been impossible to win auton otherwise.
I do think that a lot of the rule ambiguity comes from the GDC putting “at the end of the match” in their definitions without really thinking about the implications that has. They’ve done so for previous games, and nobody even considered that this simple phrase could break scoring after auton, and so there wasn’t any issue. But this year we’ve noticed what this phrase could mean for auton scoring, and so thus begins the confusion. Are “at the end of the match” phrases intentionally put there by the gdc to only count at the end of the match, or were they just written like that because they’ve written scoring rules like that in the past and just didn’t think about what that actually means.
It’s impossible to know currently, because there are hints that could be taken in favor of either scenario.
@9MotorGang points out here that in the game video, it does show alliance goals being counted for points at the end of auton, despite there being an “at the end of the match” condition for these points.
But on the other hand, they answered that no, elevated robots and goals do not count for points at the end of auton in that Q&A.
So it’s really unclear what they intend to count or not at the end of auton.
But, as the manual currently stands, anything that relies on being “at the end of the match” to count as scored cannot legally be scored at the end of auton. It’s entirely possible that the technical rules of the manual don’t line up with the intent of the gdc, and since we have no clue what they intended, we have to take the literal definitions in the manual for now.