To me, having either or both of those bonuses available is equally interesting, as long as something makes it clear how the bonus works, for example by having the bonus being "+X% to the Shield Section" for the section-specific bonus and "+X% to shield-related stats" for the Exo-wide bonus.
"One question is whether it would continue to apply the +% to your base health (which is a shield-related stat)."
I would say that, for a section-specific bonus, I would only apply the bonus to components in that section, primarily because I can't think of a base stat that could come from the Propulsion section. I can see Power from the Reactor section, Health from the Shield section, sensors from the Computer section, damage or ammunition or range or splash from the Weapon sections, but I can't think of anything from the Propulsion section, which would make that bonus inherently weaker if section-specific bonuses were applied to base vehicle statistics. For Exo-wide bonuses like +X% to shield-related stats, I'd be fine with it applying to base vehicle values.
Speaking of these bonuses, though: is the following more or less correct and complete?
* Shield-related stats: regen, regen window, shields, system protection, damage reduction
* Weapon-related stats: damage, range, splash radius, ammunition
* Computer-related stats: hacking points, virus points, sensors
* Propulsion-related stats: stealth actions, consecutive stealth actions, trap avoidance
If not, what's missing and where does it go, or what should get moved?