Happy to help! If you open up Apple's TextEdit application, you'll notice that the Format menu there pretty much exactly matches OmniOutliner's. That's because both TextEdit and OmniOutliner are built on top of Apple's cocoa frameworks - there are a certain number of features OmniOutliner gets "for free".
The default cocoa-framework version of the subscript and superscript commands live under a "Baseline" submenu, and those commands do just that - they modify the baseline of the text but not the other properties.
I'm not sure if we have a feature request open on versions of those commands that formatted other parts of the text style, but if it would be helpful for your work to have them, send email to our
support ninjas; if there's an existing feature request, they can attach your email so the rest of the team will know you'd like to see that added.
(The number of customers requesting a given change is one of the metrics we use to plan the work on our products.)