Should optimize animation "actively" do anything?

i was just wondering, in an animated gif, should the optimize animation settings in cs5 (both bounding box and redundant pixel removal) "actively" do anything? by "active" i mean affect or alter the frames in any way after clicking "Okay" and prior to saving.
i was just asking because i saw this gif on tumblr and all the layers but the first have a lot of transparent pixels, which i feel is what photoshop should be doing with my gifs if i'm correctly understanding what the optimize animation settings do. all the animated gifs i've made thus far always lack any transparency even though some of the pixels are exactly the same.
here is the tumblr gif i was talking about:
and yeah i know it's pokemon, whatever, don't judge me

Thanks for you prompt response, Steve
Sorry, i should have made it clearer in my posting.
I am creating these animations externally (from another tool) such that they can be viewed using Acrobat.
I know it can be done with U3D because the format supports animation. I can create the u3d info from my application, and store it in a PDF container.
I was wondering if the same can be done for PRC - does the format itself support the concept of animated entities - i.e. parts moving (and perhaps other properties changing) over time? 
-dr

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