Walter,
You can do that. I would use maybe 15 to 10 pound. I have found that when fishing shallow water zones I like to have a longer butt section. I like to do this because I can grease it as Davy showed me to make it float and to use it for easier strike detection. Also, when fishing shallow you need less weight and there fore the butt section can be used to keep your flies shallower.
For deep water nymphing I have been using a 3 foot section of 17 pound. I like to use more tippet when fishing deeper water types. of course I am not using a strike indicator when fishing.
If I were using a strike indicator I would have the standard 5 foot butt section at all times. the section that I would modify would be the 4 foot section. I would do this depending on the water depth that I am planning to fish.
I would venture that the butt section does not affect the rod much. Remember, the fly line has a much greater diameter then the amnesia. I would say that the indicator and the shot are having the greatest effect with the shorter/lighter rod.