I wanted to do the same thing and tried, but they're right, there's a dozen or so holes for the clips down the length of the rocker panel, not an area that I would want to have putty/filler.
"should've bought the "sport" model"
oddly enough, I couldn't find a 5spd sport when I was buying. Seeing how I don't like the side sills OR the climate control (but I do like the 2nd row pullout table) I would have been better off with a Sport.
Most Sport models have the side sills anyway. For some reason Mazda, or the dealers, think most people want these sills.
Since I actually own one of about five US Sport models without the sills, I can tell you that the "holes" have some sort of body-colored plastic insert that fits flush. I wonder if it's possible to acquire them somewhere. After that all you have to do is remove that rear spoiler...
thank you doctorz! you don't know how hard I tried to find the answer to that question: what about the holes! my stunningly unhelpful dealer parts counter didn't help and like you said, all the Sports I came across had the side sill package. I have a new mission: body colored plastic inserts. my wife is going to be thrilled! lol
the reason I know about those inserts is that properly installing the mud flaps require removing one of them. I noticed a line of them, and I guessed at the time that they had something to do with the side sills.