The Shots continued their impressive form under Scott and went ahead through Craig Reid's opener but Leon Legge levelled for the Gills with a 75th-minute header.
Scott followed up last weekend's victory over Fleetwood with a hard-earned point at Chesterfield in midweek, and this draw preserved his three-match unbeaten record since taking the reins.
He said: "We're just disappointed that we've only got a point and to say that against the league leaders, who have only lost once away from home, shows exactly the mentality in the squad at the moment. That's exactly what we're trying to harness.
"In the first half we defended fantastically well. We needed to link our play better, we were a bit sloppy and we needed to slow down when we won the ball. There's a tempo you need to play at, you've got to calm yourself down and use it.
"I'm disappointed with the sloppy goal we've conceded but after three games we're nit-picking about throw-ins and things like that, I would have settled for that from the first day I walked through the door."
- Sports & Recreation
- Leon Legge