I do believe Rossi received special attention, but I don't believe for a minute Honda would be willing to try anything radically different or experimental on the champ's bike for obvious reasons. The differences must have been minor IMO.
Same with Yamaha, I bet right now they are all on exactly the same machinery, after all they want to gather as much testdata as possible. It doesn't make sense to have one bike which is fundamentally different from the others, it slows development instead of speeding it up.
On a sidenote, I agree with you that Biaggi deserves more credit than he's getting on this forum, he's a fast and very smooth rider, and still the only one to win on an M1. He's no quitter either, I remember he lost the front end a couple of times on a row (in different races, a couple of years ago...), he just got back on and finished the race every time, except once when his bike was totalled...
However, while Rossi and his team are in a league of their own when it comes to setting the bike up and choosing tires, Biaggi and team still pick the wrong tires or settings every now and then, and unfortunately Biaggi seems to think that's something he should complain about instead of feeling responsible for it.
All in all, while I don't think he is as good as Rossi, he is a great competitor, and one of the best of the rest ;-)