If you are wanting to add a program to the Windows registry the process would be better done by creating an installer program. It is all too easy to trash the registry if not done correctly. A trashed registry can result in Windows not working or booting.
I could be way off, but my very limited understanding is that the registry is not useful here.
If an executable program type (includes libraries and more) is dumped anywhere onto your disk, the antivirus scans it against its search algorithms for bad stuff. It does not care if it has a registry entry or was properly installed. It does not, to my knowledge, check the registry for this (it may check it for auto-startup and other known virus signatures, but not installed programs).
Think about it, what would a registry entry prove? If all it took to convince the AV that your program is legit is a registry entry, don't you think malware would have such entries?
So the bottom line is that if your AV is of any value, yes, it will notice that you put a program on your machine and it will check it out. This will happen whether the program is 'installed' and 'registered' or not.
it shouldn't matter. plenty of things auto start without tripping AV. Adding to ignore list will work on one machine, but in general, if that file later gets infested it will be big trouble to track down because its on ignored list. Auto start is valid and won't trigger AV unless the program being started also triggers the AV's scans. Now if you auto-start via a root-kit or some other nefarious approach, that will get some attention.