He's nipping it in the bud with all sorts of passive/aggressive comments instead of saying "No, we don't work on boots not bought in a dedicated ski shop."
Or, if he wants business, saying "Most people buy boots that are too large, so if you come in there is no guarantee they'll be appropriate for you, despite how they feel now. I can't work on them if they're not the right size and shape for your foot, and our minimum fee of $X would still apply. We can look at other boots during the time if that happens. In fact, I'd want to start from scratch checking you, your feet and thinking about what's best. Bring in your current boots in case they do work for you. Then we can move to footbeds or other tweaks. Can I schedule you?"
I mean, this isn't rocket science (the customer service aspect) - especially if it happens a lot. If it happens a lot, develop a script that works most of the time. Then be more obnoxious for the ones that don't listen.
And this "Thats a brand that we sell the least of. Most people find those boots are the least comfortable of the brands I sell" should be "Wow, I'm surprised because those fit very few people's feet; I'd want to check if they're right for your foot. If they're not I'm sure we can find something more appropriate; we have 27 other boots." It might feel a little "upselly" but that's what the shop should want to do, right?
Though maybe being a dick is the script and they want a reputation of being prickly so other people don't come in. But I sure wouldn't come in even to buy if I heard that story.