1. Yes, the defense can still tag him out. In fact, until the runner shows no attempt of returning to HP immediately after passing it, the defense has to tag him instead of being able to just touch HP.
On a tag play, yes, you would have a valid complaint b/c of what the mechanics are suppose to be. It isn't going to change anything, but you have a valid complaint. It's not protestable.
On a force play, no, you would not have a valid complaint. The umpire has to signal if the runner is safe or not due to the dynamics of the rest of the potential plays based on the outcome of that.
2. Run scores until appealed. Once the runner passes HP, he is considered to have touched it until properly appealed.