It was stored by character since it's quite likely that each character is a different class; not storing by class since your alts likely want different skills shown depending on level/spec/ect. Enabling Demoralizing Shout or something class specific, then copying that profile to your mage isn't terribly useful. However, extra settings should probably be saved by profile instead.
I'm interested in trying other bar addons as replacements for Sorren Timers + CooldownTimers 2. However, I haven't seen any others that I like better. RBM looks interesting but I can't find any good documentation, so I have some questions:
I haven't looked at it since Apoco took over, but I'll answer what I can since I built the core.
3. All settings are changed immediately, no reloadui (unless you reset your profile).
4. Uses SM-3.0, and all texture, sound, and font options come from it.
5. Has transparency options for the base frame, which in turn affects the bars.
6. What text: no not really, that's up to the individual plugin (some may offer customizable text, others not). Where: yes, it offers full support for alignment and offsets of the timer and label that are independent of each other.