Yeah, I agree, it definitely affects the tactics.
Otherwise, we wouldn't be asking "stupid" questions here and "bothering" the organizers, would we?

Furthermore, as far as I remember, the rules initially stated
that the final save could contain one secondary hero.

So, the question is only about the "stuck" heroes.
Perhaps those who had already submitted their save and whose hero was "stuck" replayed to avoid this.
And now, such heroes are allowed to remain, and even a "stuck" hero will be counted as the best if its stats are higher.
But, I think in such a case, the participant would most likely have contacted the organizers with a similar question, as you did.
Apparently, you were the first to encounter this situation. And I was the second. :D

In any case, it is better to contact the organizers again and request clarification of the rules (not a change),
than to submit the final save and then regret that you
interpreted the rules in your own way, while the tournament organizers interpreted them in their own way.