I'd personally be mildly annoyed if people in my clans were killing indie merchants just because they were mastercrafting things, in general. Most traders in the world are, indeed, independent. In Allanak the bazaar is lined at the edges with GMH holdings, but you can clearly see that the vast majority of the space is dedicated to NPC and vNPC traders that are making their living on their own.
So what sets apart those indie traders from their GMH counterparts? Here's just a few things:
- Specialty. Salarr's focus is high-end weapons and armor. Kadius relies on high-end clothing, jewelry, furniture and other luxuries. Kurac has spice, of course, but also spice paraphernalia and high-end travel gear. Indie merchants might find it risky to tread into this territory. That's not to say they couldn't design weapons, armor, etc. It just might not be as good.
- Supply arrangements. When House Fluffypants needs 100 pairs of diamond-encrusted, feather-lined pantaloons, they don't commission a new design with Amos the tailor, who works off of a blanket in the middle of the Allanaki bazaar. They go to House Kadius. Indie merchants might find it risky to set up major deals with major customers.
- Time. Salarr, Kadius, and Kurac have been around since the rise of mercantilism. Your typical indie merchant has been around since they were born. A typical Zalanthan lifespan does not compare well to 600+ years of existence. Indie merchants might find it risky to suggest that they're better, or even comparable, to these huge entities - at least until they actually are comparable, by becoming the leader of a Minor Merchant House. And even then it's a long road to becoming better.
So, my advice: know your PC's place as an independent and they'll be fine, at least as far as GMH ire goes.