With 5" BS you should get back inside the flares. I know my 03 came with rims that were 5" BS and they were inside the flare. But when moving up in tire size (at time goal of 33's) I went with a 16"x305 (roughly 12.5 inch wide) rather then a 16"x285 (roughly 10.5 inch wide) and had rub problems in the front at full lock one way or the other. The fix for me was to install three flat washers behind each of the steering stops. Later I went to a 15" rim and 33x12.5's on a roackcrawler 3.75" BS. With that set up I had ZERO rub and plenty of play. I went ahead and upgraded and am now on 37x12.5x15. So far I have no problems except on full stuff I get a little rub in the rear. FWIW I started at the same point you are at with the BBL, I also added a Nth TT, Tranny Skid and OPSkid, with a set of used 305x70r16's. This was the set up I used on my first trip through the Rubicon trail and it worked very nicely. Here is a pic of my flex on that run.
04 trip on BBL and TT
05 trip on 33's and the RE 4.5" LA
IMHO other then the rear loading on the early pics there is no difference in ride height between 04 and 05. One other note related to 04 is that I did replace my stock LCA's and rear UCA's with a set of Nth stock lower replacements (2" x .250 square tubing vs. waffled 1/8" stockers) and adjustable rear uppers as I went with a CV shaft righ away.
Best of Luck to ya!!