As far as I'm aware there isn't any way of optionally ignoring the additional word characters specified in Preferences when trying to select words.
I'm often wanting to copy, change or set search selection, part of a variable name which doesn't include a dash, underscore, etc., though most of the time I do want it to include those elements as part of a single word.
One solution would be to use a modifier key: So, in my world, Cmd-Opt- Shift + Right or Left arrow would ignore the additional word characters and Cmd-Opt double-click and Cmd-Ctrl W would also work the same way (there may be better modifiers!)
The alternative would be to toggle the additional word characters option in the Edit menu, which would have the downside of not allowing you to dynamically change your specification in mid- selection, but may be simpler to implement.
I've wanted this for a long time and am surprised it hasn't been suggested before (as far as I can remember) which probably means a) that the functionality is there and I just haven't figured out how to open my eyes yet, or b) it's a really crap idea.
Any thoughts? James