not sure what you mean by a healing cap. I had a white plastic "cap" that held the bandage on my BAHA site post op, but once the doc removed it I never saw it again.
Why would you want to put it back on?
Or, am I confusing this "healing cap" with something else?
Regardless, I think the answer to your question is, as the BAHA site heals the "screw" calcifies to your skull. I never really thought of it before, but I'd imagine that might "displace" the screw a little. Not that that's a bad thing.
I can also tell you from touching the screw in my skull (just now) that the top of the screw is closer to my skull than the bottom of the screw. The bottom is by no means far away from my skull, but it is defintely farther away than the top is. This is because when you eventually get to snap on your processor, there will be a little room between your processor and your skull. If your processor was right up against your skull it would cause irritation to your skin - and it might even cause the processor not to work properly (I think - I'm not 100% sure of this last part).
Bottomline, I think everything is fine. The way your BAHA site was immediately post op (remember the "divot"?) is not how it will ultimately look once your 90 days are up and everything has healed. You'll see changes, but that's the way the surgery is "designed".