how is it that two engines with the same capacity(cc) have different power outputs(bhp)?

Answer 1

All these can affect bhp for the same displacement:
- different compression ratios
- different fuel injection systems (carburation or fuel injection)
- different exhaust manifold shapes and volumes (not to mention mufflers, cat. converters, etc)

There are other things as well.

Answer 2

i'm with "tlbs101" (above), others thing to create this difference would include; turbo charging, super-charging, changing the lift/duration of the cam, larger intake/exhaust valves, or "mds" jacking up the voltage and increasing the time of firing each spark plug.

there are a million things that can change the horse power w/o changing the displacement.

Answer 3

One could have forced induction(turbo, supercharger) and one couldnt, and the information of the guy above will effect it too.