Following on from my comment and Bill's answer, it's worth noting that the quote is actually (with my emphasis)
In your most humble opinion, what's the difference between...?
If I were to say "In my humble opinion...", then my opinion is not really humbly expressed at all. I think it's a good opinion, and I'm not afraid to express it.
It's a set phrase, a meme. It's deliberate sarcasm.
Calling someone else's opinion "humble" is slightly ambiguous: it could be using the same idiom where their opinion is good and they should not be afraid to express it (inviting them to say "In my humble opinion" with the memetic meaning); or it could indicate that you think their opinion really is humble.
However, emphasising the judgement with most puts the phrase firmly into the category of "not humble at all", especially in a slightly colloquial environment of email in an expert group.
That said, because of the ambiguity inherent in calling someone else's opinion "humble", doing that is definitely not to be recommended unless you are absolutely certain of your audience.