He said, that Magilante deploys builders. I assume some kind of 3D printer for buildings. I don't think he refers to a human.
Well fair. So it is not directly a plot hole. It just revolves around things not yet revealed.

It has enough intelligence to decide whom to export the tech too. And not export advanced military tech to naval powers.
Something that does conflict with earlier statements. It can be it just does not export military tech to naval powers at all.
But it seems clear we are missing a lot of information on Magilante. Just for a start what the heck the builders are.

Sure, but he's a confirmed pandemonium user. And his magic manifests differently.

From what we know to be a magic-user you have to:
A) Either know spirit magic to produce a glow (pandemonium or magic potential)
B) Use their free magic which usually glows
Does not really matter how his magic manifests. We have one clear and proven exception to the magic=glow rule.
That already means a lack of glow cant be used as evidence to a lack of magic.
Heck. We even from Garts training have more examples of people using magic without a glow.
So its not even that Spirit magic always create a glow.

While it's possible that pandemonium user never uses too obvious magic, let's weigh the pros and cons of Burk being magic-user.
I dont know where Burk enters into the picture. Im talking about this guy.
http://www.neorice.com/hoh_noah_624