It is not there, so it is not there.
No explanation is given in the Quran itself.
One understanding is that Surah 9 has a lot of 'fighting' verses, so no heading of mercy etc, though it is in the chapter.
Liking an explanation is dependent on what satisfies you intellectually and if you do not like this then find one that does.
I am of the opinion that it is not relevant for my understanding of the Quran and I do not worry/concern myself with this none problem.
I may have missed something but I thought all Quran manuscripts did not have this bismillah in surah 9?
If there are some with bismillah, then were they added by overzealous scribes and as such they are irrelevant as the vast majority show this up as a mistake and not part of the Quran.
[It is possible to add words to the Quran but everyone would know and reject the forgery due to the careful transmission both written and oral of the Quran.]