Bit odd, as I'm not aware of any vocalisations made by Trapelus species resembling the noises yours is making; then again I know little about them in general, other than perhaps basic care and whatnot. The animal in question doesn't seem to be in significant respiratory distress, but it's difficult to tell; I have noted similar noises from freshly-imported lizards and larger colubrids with RIs, but it was almost always accompanied by some other noise; whether it be rasping, crackling, whistling, gurgling, etc. Convulsions; runny discharge from mouth, eyes, or nose; and vomiting are things I've frequently noted in fresh imports with serious RIs that've "coughed", but you note nothing of the sort. Said "coughing" was more of a dry vomit-type action as well. My tegu'll sometimes make a snorting/coughing noise whenever she goes for a drink or a swim, to clear water from her nose, but I doubt that's what's happening here.
Though it very well could be a territorial threat display, it's not what I'd expect from a desert agamid species; but there's no telling what's typical of them in a captive environment. Supposedly most Trapelus are capable of hissing, but I haven't been able to find anything about abrupt noises similar to the ones yours is making. I'd still probably consult with a vet just in case; most that I've worked with would accept e-mails and/or phone calls about simple inquiries, I'd probably go that route if your vet allows.
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