1) They are, as you say, effectively the same but in a different wrapper. Some editing programs – notably Final Cut and Avid – will simply prefer the files in one wrapper or the other so you may find it more convenient to shoot thus to save you the bother of re-wrapping them prior to edit. If your editing software will accept either format without issue then your choice is simply one of three factors: disc space, computing power, and image quality.
Clearly the higher bitrate requires more disc space to store but hard discs are cheap these days so that’s the least relevant factor. H.264 is very computationally intensive so a higher bitrate means even more data for your CPU to handle thus you may find the lower bitrates and formats handled better by your PC (it depends on your computer). Finally, as a general rule, a higher bitrate for a given codec = better quality pics so that is one reason why you might choose 35Mbps mp4 instead of 28Mbps AVCHD, so as to capture your footage in the best possible quality even if you then transcode it to something else for editing.
2) There have been firmware updates for Canon’s camcorders but I’m unsure if they’ve ever done so in their consumer line. For example, the C100 has just had an upgrade announced that improves auto focus (although the camera does have to be returned to base for the upgrade so I’m not sure if it’s entirely a software alteration and the press release is vague on the matter). I certainly agree that Canon should upgrade the XA20’s firmware but whether it will bother them to do so is another matter entirely. Perhaps if enough customers complain?
3) Regardless of your ultimate destination, I would always recommend shooting in the best possible quality, partly so that your archive is as good as it can be in case you ever want to come back to it, and partly because every phase of rendering and encoding video degrades the quality slightly so the better your source footage is, the better your eventual output will be, even on YouTube.
As to the optimum render settings – gosh, what a can of worms this one is. There are pages and pages of advice all over the Internet where people have spent months analysing the “best” settings, so it’s a bit subjective really. To cut the long story short, all I would suggest is that you render to full HD 1080 / 25p, probably in an H.264 codec (aka AVC) probably in an mp4 format. YouTube likes mp4s to be hinted for streaming (this is usually a tickbox on your render settings). Use as high a bitrate as you can reasonably stand given the subsequent upload times! Eg, I render using 1080/25p at 10Mbps using Sony AVC.