...I assume the bike can never prepare you for the strain on your knees and ankles. You're also working different muscles.
I would agree with you on this. What I've found, however, is the reverse is true for me - lots of hiking prepares my muscles for long distance multi-day bike rides, like a RAGBRAI. Hiking doesn't condition my butt, however, so bike saddle time is needed for that at the very least. But, my legs and lungs doesn't need conditioning after lots of hiking.
