How to register a custom built for Kryptonite's ATPO Program?
From the Kryptonitewebsite,  looks like both the make and model are open-ended text entry forms. So I think you’d be ok to write something like:

Make: Bike-builder’s-name
Model: your-name

So if you had John Jones make your bike and you’re Carla Carlson then you could say:

Make: JJones
Model: Carlson
Model Year: 2020

If you built the frame yourself, then I think you could name it anything you want.
For kryptonite, they need the bill of sale if you bought it or an appraisal if you built it yourself.
Kryptonite is a little famous in being ... slow ... in paying out on their “insurance” so you may be better off just listing your bike on your homeowner or renters insurance policy.
What’s important to remember is that from the perspective of kryptonite, insurance companies, the police, etc is that the frame is the bike for all intents and purposes. So you use the frame number for the serial number of the bike.