I used the Yakima fixed point system, Landing Pads on the forward mounting points _both_ front and back. This gives about a 48" spread front to rear which is pretty good for carrying our 16' relatively flexible kayak. Using the forward instead of rear mounting points for the front bar also helps level the bars; the front bar is about one inch higher than the rear, not bad. After the landing pads are in place and the Yakima crossbars and towers are set up, they are very quick and easy to put on and take off. The landing pads stay on the roof, they are fairly large and noticeable but I got used to it. Once they are in place I don't want to be taking them off and putting them back on, they just stay on the car and it's ok.
I drilled holes in the trim strips for the bolts to go through to hold down the landing pads. It was a bit tricky to mark and drill the strips in the right places and I had to drill out the holes pretty large, but the landing pad totally covers them up so no worries. It's nice to keep the trim strip all in one piece. Also I bought a set of nylon spudgers at Harbor Freight for like five bucks and they are invaluable for prying loose the strips without worrying about nicking paint. Also useful for interior trim such as popping off the dashboard speaker covers.
For carrying a rooftop ski box, the 48" spread is too wide--the clamps on the box don't spread that far apart front to rear--and while using the rear mounting points for the front bar would make the spread about 42" and the box could mount to them, it would be so far back that it would hang past the rear hatch. So, I used 3/4" (ID) galvanized pipe (close to same OD as Yakima bars) and Kee Klamps to make a set of front-to-rear rails with a single crossbar that can be slid to desired location and tightened down. The front mounting clamps on the box attach to the front Yakima crossbar, the rear clamps attach to the pipe crossbar and I can put the box exactly where I want it. Works great, although without the box the setup howls and costs about 3 mpg. I had to spend some time on the pipe setup, had to grind the openings a bit larger on the Klamps and round some edges, but eventually got it to work and now it's not too hard to put on and take off, although there are bolts and setscrews to deal with. I used four Kee Klamps type 16-5 for the rails and two type 10-5 for the crossbar. Not cheap but they work and are unobtrusive in appearance. Got them from Simplified Building Concepts.
While I at first was annoyed that this Mazda did not have good full-length roof rails like my old Passat Wagon, this setup now that it's been worked out is pretty good--it's a lot easier to remove the crossbars now than it was with the Passat.
You mentioned cost--the Mazda rails aren't that bad price-wise; I think you'll end up spending a few hundred no matter which way you go. I carry a boat or a long box, so my setup works for me. If one were carrying bicycles or similar that needed a shorter spread, the factory rails with aftermarket crossbars might be a better choice.
