Consider two men:

Person A: Runs 2.5 miles 3 times a day. 29% body fat. Relatively
sedate the rest of the time.  Low cholesterol, low blood pressure,
generally healthy.  Eats whatever they want whenever they want.

Person B: Doesn't overtly exercise but is very active on the weekends:
gardening working around the house, shopping.  26% body fat.  Low
cholesterol, low blood pressure.  Watches their diet and doesn't eat
too much.

Who is healthier?  Or more specifically, does person B's active
weekends replace the need for exercise, or is there some latent
benefit (besides weight loss) that over exercise gains more than just
spending all day on your feet?

Is everything else equal?  There are a variety of additional factors
that can influence one's health.  For example, emotional stability,
genetic make-up, environment, habits, etc.

Person A runs 3 times a *day*???  Aside from possibility that A is
overdoing it, I'd say A should be healthier.  Aerobic exercise is
helpful for the cardiovascular system.  B gets some exercise, but it's
probably not aerobic.  And eating whenever he wants isn't necessarily
bad.  Eating many small meals is often recommended over eating 3
larger ones--helps keep the metabolism rapid.

Er... sorry, person A runs 3 times a week.
Also assume all else is equal between the two people, they're in their late 20's.
The question really boils down to is if there are some people who are
gentically fit enough to not really need to exercise.  When you say
"aerobic exercise is helpful for the cardiovascular system", can you
clarify what that means?  If person B is not overweight and not
overtly at risk for heart disease, why should cardiovascular health
matter?

Person A is way healthier.  Regular cardiovascular exercise makes the
heart stronger, and also promotes good blood flow throughout the
entire body.  It also helps the immune system and digestive system by
keeping the body moving.

Compare resting heart rate and jogging heart rate and you'll see a few
of the benefits that person A has likely already obtained that person
B has not.