Scotland are likely to be without both Finn Russell and Adam Hastings for the Test match against Tonga at BT Murrayfield on October 30.
The game, the first in the Autumn Nations Series, falls outside the international window and there are league matches scheduled in France and England that weekend.
It means Townsend’s squad to take on Tonga is likely to comprise players drawn from only Glasgow Warriors and Edinburgh.
Wilson has picked Thompson to start for Glasgow against the Lions at Scotstoun on Saturday, with Duncan Weir on the bench following his recovery from a concussion sustained against Ulster.
The Warriors coach thinks both men will come into contention for the Tonga game, with Edinburgh pair Jaco van der Walt and Blair Kinghorn also likely to feature.
“They are definitely in the mix for an opportunity,” said Wilson of his two stand-offs. “I certainly think Ross and Duncy over this past period have put their hand up and have good performances.”
Thompson, 21, was called up by Scotland in the summer but was denied a first cap when the tour to eastern Europe was cancelled due to Covid. Wilson believes Townsend would have no qualms about selecting the relatively inexperienced Glasgow fly-half.
“He is certainly bold enough to go with Ross,” said Wilson. “If Gregor thinks that is the right call he will make that decision and he will be comfortable with that. I suppose it is more based on form going into it, which right now puts him in a good place.”
Glasgow blew the Sharks away in the first half last weekend to notch their first win in the United Rugby Championship and Wilson will be looking to maintain the momentum against the Lions.
He will have to cope without Scott Cummings who has undergone surgery after damaging hand ligaments against the Sharks, ruling him out for six to eight weeks and causing him to miss the autumn Tests.
“He played on with it,” explained Wilson. “He functioned all right - I suppose adrenaline kicked in. It wasn’t until after the game that he reported it a bit more, saying he was struggling. And then, as happens, he woke up the next morning and it’s a hell of a lot worse.”
Lewis Bean comes in for Cummings in one of two changes to the pack. The other sees the return of Rory Darge who has recovered from a knee injury and replaces Tom Gordon.
In the backs, Nick Grigg is picked at outside centre, with Sione Tuipoluto on the bench. Wilson said the decision was no reflection on the latter’s performance against the Sharks.
“He is certainly not dropped,” said the coach. “He was outstanding for us on the weekend and since he has been here but we must make sure we manage him as he had a couple of little bangs.”
Jamie Dobie is given the nod at scrum-half ahead of George Horne, who is among the subs.
Meanwhile, Wilson expects Zander Fagerson and Ali Price to return to action in the Leinster game on October 22 following their graded return after the British and Irish Lions tour.