Reid Park has been a happy hunting ground for Triple Eight over the years, while opening practice on Friday and Sunday's chaotic race were hit by rain.
Asked if the team could get an accurate read on developments even with those caveats, Dutton told Supercars.com: "Definitely. Very positive.
"We came here with an overarching plan of what we wanted to do and what we thought would work for the car. It did.
"But as always what you don't always know is the magnitude of the side-effects of those set-up changes.
"We sort of predicted what side-effects would come and they did, good kudos to the engineers there by saying 'we think we're going to have to deal with these issues by going in this direction' and they all came true.
"It was still a faster car so it was the right direction, it was still an unrefined car, one you'd love to have here for a test day.
"Usually one of our big strengths is our kerb-riding ability and we lost a bit of that this weekend.
"That was one of the side-effects from the stuff we were doing but overall we had fast cars so it was good."
An early undercut and pace in clear air gave Whincup the lead on Saturday, until he was overtaken by points leader Scott McLaughlin in the final stint.
Van Gisbergen finished that race fourth, and won his and the team's second race of 2019 a day later.
Whincup was among the quicker cars in Sunday's greasy conditions, but crashed shortly after making his first pitstop.
Dutton highlighted one-lap pace as an area for improvement, van Gisbergen having started fourth and seventh and Whincup sixth and 12th.
"Jamie loves [Townsville] and always does a good job," Dutton said.
"We still didn't have the level of consistency and pace we wanted in qualifying. Obviously that's evidenced by Jamie not being in the Shootout.
"Race pace, we've been very strong the last few rounds. Darwin, particularly, Jamie was very strong.
"Both cars were strong [on Saturday], Jamie's was exceptionally strong in those slippery conditions [on Sunday].
"I truly believe, all things being equal, that he would've been next to Shane; whether in front or behind or beside, they would've been racing each other.
"It would've been nerve-wracking in those conditions but it would've been a great problem to have.
"In those slippery conditions, he was doing a stellar job."