Apologies--I missed this on its first go-around too. That doesn't mean I'm not opinionated on the subject.
I used Bringhurst when working for a design publication; I used a designated big honking typesetting machine (I still miss that solvent smell!). In fact, part of my job was to look for and fix things like what is being described here (different digits require different amounts of padding, plus it varies based on the individual typeface). I used the AP Stylebook when working for newspapers and other publications aimed at contexts that have limited typesetting and are read quickly for content rather than savored for the art of design. I also have a fondness for the journalism stylebook approach. Different tools for different contexts.
Fond as I am of Bringhurst, CPDL should generally follow a journalism stylebook such as Chicago over Bringhurst. If we operated in an environment where we had the luxury of having a typographer adjust the spacing between the specific numeric digit and the closing parenthesis, then by all means we should follow Bringhurst. On CPDL, however, it is not scalable or desirable for us to make this type of microadjustment. Furthermore, the reality is that the content is being rendered by various browsers, some of which choose to trump the font for preference reasons, and some trump the font for disability reasons.
The goal of CPDL is to make the information readable at first glance for the most (ideally all) people. Therefore, we need a solution for parens that works generally without collisions. The proper solution in light of CPDL's environment is to keep the italicization consistent to avoid collisions when a user's browser renders the information. The best way to avoid collisions is to keep the italicization consistent between the parens and the text they bracket: either all italicized, or all not italicized. If parens have to be placed inside a non-italiicized sentence, it's more important for the parens to match their inside content and not collide with inside content (which could contain text) than for the ending parenthesis to avoid colliding with the punctuation following it if that's what follows it rather than a space.
I'd be interested in hearing other views.