It seems like you’ve already decided to go with an online jeweller instead but I just wanted to add that I don’t think it’s a red flag. Jewellers are often wary of what they don’t know about because they might not be sure if it will turn out well, and feel that the stones they’ve worked with for many years are the “best”. They usually take pride in their work and want to make sure they produce the best product, so they might be understandably hesitant to use something they are not familiar with.
Just to share my experience: I had my moissanite ring custom-made by a local jeweller. I considered doing it online but I decided I really preferred getting it done at a place where I could easily go get things modified (e.g. if I wanted the finished product filed down in a certain place or modified slightly, I could just bring it back myself instead of dealing with online shipping back and forth).
Anyways, I actually specifically picked a jeweller who dealt a lot with moissanites. However, they had always used the C&C Forever One round brilliant, and were not familiar with the new H&A cut (and did not know the difference). I honestly didn’t hold this against them because I don’t expect them to know everything. I wanted a 3-stone ring, however C&C do not make H&A-cut moissanites in the smaller size I wanted for the sidestones. As a result, I decided to source my moissanites on my own online from MoissaniteCo.com and bring them in to the jeweller to get them set. (I liked the higher crown of he H&A stones, and wanted all three stones to match.)
My jeweller strongly discouraged me from doing this. They were very skeptical about the quality of non-C&C stones and highly recommended that I just get the regular F1 (non-H&A) for the sidestones. They were nice about it though and explained their reasoning (apparently in the past a client had brought in her own non-C&C moissanites and they were much more yellow than the F1). But even after I sent them a video of the stones they were skeptical and said that it could be difficult to tell if a stone is yellow from a video due to different lighting etc. However, I had done my research and I knew it would look great so I was firm on wanting it done this way. After I insisted, they were fine with doing it my way (although they did charge me ~$100 extra for me bringing in my own stones, which I was ok with). Throughout the whole process they were still very professional and polite, even though they disagreed with my choice. (And btw, once they saw the stones in person they absolutely agreed with me that they looked fantastic!)
Anyways, I know my situation is not the exact same as yours but my point is, I don’t hold it against a jeweller for not being totally familiar with other stones they have never worked with in the past. If they still put up a protest after you firmly state your preference, then forget it. But if they remain polite and professional, no reason not to go with them if you love their work.
Btw, although I disagree with that email you received (I don’t think there is anything rare or special about diamonds compared to other gemstones–the whole idea that they are more “special/rare” is PURELY a marketing gimmick), I do not find it to be that rude. Just unknowledgeable about moissanites (but since diamonds are so much more popular, I find this to be forgiveable). The tone of the email was similar to the one my jeweller sent me–it’s easy to find it “rude” because they are unknowledgeable yet treat YOU like you’re the unknowledgeable one (when it’s the complete opposite). However if you take a step back, the email is still quite professional and simply them advising you on their opinion (which even though it’s wrong, I understand where they’re coming from).
Just my two cents!