But it’s just as likely the two ships would encounter each other as such:

This could cause some confusion.

The only way to explain why different star ships always meet each other right side up is to postulate some sort of galactic standard. But this wouldn’t explain all the alien civilizations the Enterprise discovers that also fly at the same angle. This could have made for great story lines where alien races are offended by the upside down approach of the enterprise.

However, it bears mentioning that at least one species is an exception to this phenomenon.

no one can upside down the borg

Because of their simple ship design the Borg cannot be flanked, dropped onto or attacked from behind. The Borg have assimilated all three spatial dimensions into their ship design and they always appear right side up.