I don't think I would go with the clear. You would be able to see dirt and road grime under it but I do like it and am also thinking about some myself that would match the paint.
I used to have the thin U shaped rubber guard strips in clear all around the doors of my ST. They turned yellowish after about 4 months in the Texas heat/sun. I took them off and installed black ones.....it's been about 1 1/2 and no problems what so ever....they blend in with the door lines of the ST so you can't tell they are on unless you look specifically at the edge of the door trim. My girlfriends Mitsubishi Outlander came with clear tape guards (similar to the e-bay product) and they are starting to turn yellow and spider crack. The Outlander is going to be 3 years old.
I have the black on mine, The universal fit stuff from pep boys. Been 3 years now no trouble at all... JUST make sure there is no wax in that area and install on a hot day....
Over time they will scratch the paint very much like a aftermarket bra does. On all our cars I put .75" paint protection film strips. You can't see it unless you 6 inches from the car and it will not harm the paint.