If I understand you correctly, you personally know that the kiltmaker in question can make what you want for less than Scotweb or Heritage of Scotland, and it will be a quality kilt. If that is correct, by all means get the less expensive kilt. From what I've read of Scotweb, their kilts are certainly worth the price that is paid for them, but I don't think that Nick and crew would begrudge you buying a less expensive kilt from someone you know personally.

Okay, I'm not being absolutely clear here. If quality is verifiably equal, I should think that no, reputation would not be worth it. Besides that, there isn't anything to stop you from getting a kilt from Scotweb or someone else later.