PP,
I would suggest a floor system, for numerous reasons. The most important one being your body. It is much easier on your body to pull an object from directly in front of you. How many times in a drift do you pull up your anchor? Depending on your flavor of fishing, it my be a dozen or more. Try pulling your anchor up a dozen times in a row. With a side mount, a person obviously needs to turn his upper body slightly to get a good pull on the anchor. It may seem like an insignificant detail, but we all know someone with a bad back caused by a repetative strain. With a floor system, the motion is much more natural, using your whole body, much like rowing.
Secondly, addressing the rollers, with the side mounted system the rollers must be placed at angles that are not in perfect allignment. This, due to the arch of the side of the boat. Also seemingly insignificant, the pressure of the anchor rope constantly pulling slightly sideways on the rollers will in time(years), cause the rollers to wear out, becoming loud and annoying you and other anglers.
With the floor mount, all the rollers are in perfect line with the stinger that is in the middle of the transom. Mounted correctly, a person may be able to use one less roller(less resistance).
Personally I like to put "stuff" in the trays on the side of my boat. (fish club, towels, thermos) With the pulleys and dawg on the side mount, it will make that part of the boat off limits for convenient storage.
Yes, this is a exhausting explanation, but I feel my boat and equipment is an investment. Not only financially, but in time, and pleasure.
May I also suggest a lighter rope than most boat manuf. install. Personally I use a 3/8" dia. rope. Less roller resistance and less resitance in the current. You'll find your anchor will be able to hold you in stiffer current...