First of all there is no argument about it, Austin was without a doubt more popular than the Rock, lets not kid ourselves Crock.
Yeah, I think in theory Austin/Hogan would have outdone Rock/Hogan. I mean Stone Cold Steve Austin vs Hulk Hogan is the biggest match that is possible in wrestling history period. These two are the biggest draws and two most popular men in wrestling history and there is no debating that, it is the man who put the WWF on the map vs the man who saved them from dyeing at eh hands of WCW. Theoretically it doesn't get any better than that.
Wether or not it would delivered on the same level as Rock/Hogan is questionable though. In that time period (2002 onwards) Austin seemed pretty disinterested to me, Rocky on the other hand was on top of his game. I also question how the crowd reactions would have gone, as we all know Rock/Hogan's greatness is 95% based off the whit hot crowd, the in ring aspect was pretty average. I am not sure the crowd would have reacted the same way if Austin was in the ring and not the Rock.
Overall, I think in theory Austin/Hogan SHOULD have outdone Rock/Hogan but a lot depends on how the crowd reactions go as either way the in ring aspect would probably be pretty average. It is possible and even probable the crowd could have been even more white hot for Austin/Hogan so I think yes it would have out done Rock/Hogan.
Austin was not more popular than The Rock in 1999, everytime they were in the ring together when Rock was a face that year fans chanted for The Rock before they chanted for Austin, it happened multiple times, as a matter of fact here are the multiple times:
1. Unforgiven 1999 6 pack challenge-Fans were chanting only for The Rock all throughout the match. Austin didn't wrestle but he didn't have to, there were times fans chanted for Austin when he wasn't in the ring wrestling.
2. Raw is War following night-HHH hits Rock with a chair and taunts Austin, fans chant The Rock's name despite the fact HHH is taunting Austin.
3. Raw after No Mercy 1999-Austin and Rock have a confrontation and Austin and Rock are about to go at it, the crowd was clearly more on The Rock's side.
4. Raw where they teamed up against New Age Outlaws-Fans only chant for The Rock throughout the match, despite the fact that there were no heels during the match (NAO turned heel afterwards).
5. Smackdown where Arnold Schwarzenegger guest appeared-Fans only chant for The Rock throughout the match, Austin didn't wrestle but like with the 1st example, he didn't have to.
Maybe in late 2000-early 2001 when Austin returned he was slightly more popular, but that was because Rock began watering his character down from the year before. The "arrogant" Rock was pretty much gone by the fall of 2000, if you watch a Raw/Smackdown of The Rock from late 1999 and one from late 2000, The Rock was completely different while Austin was pretty much the same.
Remember how even when Rock was a face in '99 he was talking trash by the commentary during a match, when he made his entrance he would pause and look at the fans before walking down the ring, or his turnbuckle pose where he was "smelling what the fans were cooking" by late 2000 all of these characteristics of The Rock were gone, he started becoming a bit more generic, in 1999 he had that "edge" that made fans choose him over even Austin.
When both were babyfaces at the same time, Rock was more popular than Austin was.