To me this is a very simple reason. It is because Nechung is not enlightened. Thus, when Yudronma takes spontaneous trance, she does not pay homage to Nechung as well. As they are of the "same" or even lower.
With that said, even though it is an enlightened protector that is taking trance at that point, they will be able to take spontaneous trance as well. The entities that enter, will definitely be entities that do not mean harm. They will only be around to get the blessing from whoever the protector on the throne is.
I have seen videos of Dorje Shugden trances sessions where there are mountain gods that take spontaneous trances as well to get the blessing from Lord Dorje Shugden.
Thus, I do not think that having 2 protectors taking trance at the same time is something weird or not seen of. As in the CTA, at times, a few oracles will be around to take trance of different protectors at the same time.