I tend to agree with Temo on this one. I personally hate any inline CSS or html align in the actual skin file. I prefer all my skins to be nothing but pure XHTML.
How many module use cases are there were the end user is going to want to change the alignment. The only major one I can see is the Text/HTML module (I am sure there are others). However, in any module that utilizes the TextEditor, the author can control the alignment from within the TextEditor (Content) rather than artificially altering the skin (Layout) via the module properties. If alignment were critical for some reason, I would even go so far as make a special Container just for that use case.
If I had my way, I would remove all the skin altering options from the module options. Alignment, color, border, etc should all be defined in the container. Yes, I realize it gives the end user more flexibility, but at the cost XHTML compliance so the skinner can save a few steps. If its important enough to change the module setting, I think its important enough to make a custom reusable container.
While we are at it, I would also remove the Body Background setting from Portal Settings.
Of course, all of those would be breaking changes for some skins out there, so I think the solution they came up with is the best possible given the circumstances.