The Controller and the G: Synchronized trooper must declare the same Order, declaring the same Short Skills of the Order. However, it is not compulsory that they have the same target. Does this mean that when dismounted the Zondnaut and Zonmate can shot 2 smoke templates on two different spots on the table in the same order ?
No. Only the Zondmate has a Smoke LGL on its dismounted profile. You could instead have the Zondmate fire Smoke at one point on the table while the Zondnaught shoots someone in the face with a BSG.
I read it that as the zondnaut does not have smoke grenades or a launcher in his dismounted profile only the mate can launch smoke.
That's probably why only one has smoke. But otherwise, yes. Zondmate can shoot smoke someplace while dismounted Zondnaut shoots someplace completely different with Spitfire. See also PanO's Auxilia.