The All-Star Mile was run at a slow tempo with the pace increasing from the home turn, which did not suit Atishu who was outsprinted.
However, the mare did work to the line solidly to finish fifth, just under three-and-a-half lengths from the winner Tom Kitten.
Duckworth expects Saturday's contest, with Pride Of Jenni and Deny Knowledge engaged, to be run more truly which may assist the Waller-trained mare.
"In terms of race shape, she's instantly in the back-half, regardless of Pride Of Jenni and Deny Knowledge being in there," Duckworth said.
"But the hot tempo should allow her to cruise into it and she loves Flemington, so there's a lot to like about it, but it's a seriously good Group 1 contest."
Duckworth said the stable was keeping an open mind as to where Atishu may head following Saturday's outing.
The Group 1 Queen Of The Turf Stakes (1600m) at Randwick on April 12, a race Atishu won in 2023, is a possibility, as is the Group 1 Queen Elizabeth Stakes (2000m) on the same day.
"If she was to beat them all on Saturday, there's no reason why she can't go into the Queen Elizabeth," Duckworth said.
"But we'll get through Saturday and then work out where we head."