@pgseye re: the body text changing everywhere, there's a bit related discussion here: http://support.manuscriptsapp.com/topic/97/block-quotes-and-other-short-term-formatting-changes/2
Basically, the mental model is that all elements in your document are defined with certain semantics. We intentionally leave a lot of character level formatting out (and will continue to do so). What is still missing are some required element types (such as a block quote) as well as the ability to create new paragraph styles that work within the bounds of the semantics of a certain element type. For instance, it should be possible to assign a user created paragraph style to a paragraph (but that style could not be used to apply to a section heading). This is something that we intend to get to once the block quotes have been put in place.
Specifically the case of colouring pieces of text differently, you might be interested to learn that we will be adding an annotation tool in the app (in fact we had it in the pre-1.0 betas already, just decided to still polish it some more before making it generally available).
Re: commenting and Word, comments are imported presently when you copy and paste from Word, but their formatting is not retained. It's a known issue we have documented here along with a few other Word import limitations: http://support.manuscriptsapp.com/topic/24/known-limitations-with-ms-word-importing
CEO & Co-founder of Manuscripts.app Ltd