McIlroy, the 2016 FedEx champion, who will start five shots off the lead this week, believes Thomas can take a conservative approach into the tournament on the 7,346-yard par 70 layout.
Starting scores then work on a sliding scale down to the players in 26th to 30th, who begin on level par.
The "Starting Strokes" format has been introduced with the intention of eliminating the confusion of past FedEx play-offs, when the victor of the final tournament was often different from the series champion.
When the changes to the format were announced previous year, defending champion Thomas was asked if the lack of a level playing field for the Tour Championship went "against the grain of what makes sport special". "I'm just going to try to deal with it the best I can".
"There isn't a person on the planet that's experienced this before, for the stakes it's for", Thomas said.
Thomas, who captured his 10th career title with a win at the BMW Championship on Sunday, is now in pole position at the top of the leaderboard.
The Tour Championship victor will take home $15m (£12.3m), increased from $10m previous year, but McIlroy says "it doesn't need to be about the money, it should be about the prestige of winning an event that you'll be remembered for".
Will he have been the most consistent player over the season, maybe, but one thing is clear he will have one huge smile across his face whilst the rest of us look on and wonder might that cash have been better spent elsewhere in promoting FedEx and the great game.
"It's important, but I'm just going to go out and play some good golf this week".
"I was playing pretty well", Thomas said. Sometimes, the same player lifted both titles, but on other occasions, such as a year ago with Tiger Woods and Justin Rose, there was the awkward situation of a pair of champions.
I don't think the money needs to be front and centre, because I don't think that's what the fans care about.
"I think what it says is that, one, it's really hard to get to Atlanta and the Tour Championship".
During his press conference Wednesday at East Lake Golf Club, Thomas said five years ago when he was on the Web.com Tour, now the Korn Ferry Tour, he earned an exemption to play in the Memorial.
"If the FedEx Cup wants to create a legacy that lasts longer, it doesn't need to be about the money", said the Northern Irishman.
Patrick Cantlay will start in second on eight under, while Brooks Koepka will tee off in third place on seven under. Is it to celebrate the best player over the course of the whole season?
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