I had a titanium S4 on my R6. Great looking and sounding pipe. I wouldn't say you "have to" wait, but in my opinion I would strongly recommend it. It did cause my 6 to run a little hotter since it leaned it out a bit, but it wasn't a big difference. But, since you're still breaking the bike in, why risk it? Keeping the bike running cool is one of the major things they stress during break in.
Also, if the dealer you bought the bike from doesn't recomend it, you're hanging yourself out in the wind. Give your bike the first 600 to 1000 miles to make sure that there are no problems with it. If you put the pipe on and a pre-existing problem surfaces, you're going to have a hell of a time getting it covered under warranty. The dealer is going to pretty much have the final say on whether it is covered by warranty or not and since your dealer said not to do it, I wouldn't count on him backing you on an engine related warranty claim.
On the other hand, I specifically addressed this issue with my dealer before I bought the extended warranty on my 02 R1. I told him I planned on putting a slip on on it after break in and asked him if this would void the warranty. He looked it up and said he didn't think it would and then gave me a wink and said that if something happens, Yamaha doesn't necessarily need to know about the pipe when they call in the claim.
Bottom line is that it's up to you. Like I said I personally wouldn't recommend it, but part of it depends on your relationship with your dealer.