That list is to let you know what advanced/new PPTX functions may do when converted to Flash (what happens when you upload the PPT[X] to Connect). However as far as animations go, it should retain all entrance, exit, motion path and slide transition animations, as well as some of the emphasis animations. If the animations are set to on-click, then you will be able to cue them in Connect with the Next button or your right arrow key on your keyboard when the Share pod is your focus. If you have PPTX files, you should use the add-in (if you are not already), and I would just upload a presentation and see if there is anything that doesn't translate properly.
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