The tour has responded to the emergence of the Saudi-backed LIV Golf by focusing on top tier 'designated events' in a bid to bring the biggest stars together more frequently.
No plans have yet been agreed for the future evolution of those events but there have been reports that they may feature smaller fields with no cut.
McIlroy, who as a board member of the PGA Tour has been involved in those talks, says he has sensed concern among some lesser-known players about the plans.
"I've had tons of conversations with guys that are worried about what events they're going to play next year and all that. The one thing I said, look, no one's trying to screw the bottom half of the tour here. If anything, we're trying to lift it up," McIlroy told reporters ahead of this week's Genesis Invitational at Riviera Country Club.
The Northern Irishman said it was, however, crucial to have the elite featuring in such events.
"The best players should be playing in them because ultimately the PGA Tour needs to be built around the best players because that's what will maximise the value of the product," he added.
"But that doesn't mean that there's not great storylines further down that list, which we're all very cognisant of," he added.
A four-times major winner, McIlroy suggested the lesser-known players would benefit from boosting the value of the tour overall.
"If you look at like the NBA's trajectory over the last 20 years, they've built that league around their best players and their stars, not around the 12th guy on the team," he said.
"But because they've built that league up around the stars, the 12th guy on the team does way better than he used to. So that's sort of the way I've been trying to tell it," he said.
McIlroy, who can regain his number one ranking spot with victory at Riviera, said that dealing with the split in the sport had been hard to balance with playing at the top.
"It was a busy year for me, I had a ton of stuff going on, but I sort of knew going into this year that...there's still a lot of stuff that needs to be decided.
"For better or for worse, I'm part of that conversation, I'm on the board of the Tour, and I need to be a part of it.
"Would I love to just get back to playing golf at some stage? Absolutely, but hopefully after this year and the schedule's set for '24 and beyond and we sort of get everything else in place, hopefully I will be able to go back and concentrate on the day job a little bit more," he added.
