My impression is that you are not legally required to knock the building down just because it is unregistered or sold "as-is".

As-is: The seller will not clean or remove any leftover items before the sale.

Disclaimer of non-compliance with contract: This is a legal shield for the seller. In a standard Japanese contract, if a house has a hidden defect the seller is responsible. But in this case you agree that you cannot sue the seller if the house has problems.

Unregistered Building: This means the house exists physically but was never officially registered with the government. This is common for old additions or DIY sheds. While the land is likely registered, the building technically "doesn't exist".

Generally, this doesn'n hinder a parking permit. To get a parking permit, the police care only about:

Right of use: Do you own or have permission to use the land? (Your deed/land registry proves this).

Size: Does the car physically fit in the space without sticking out into the road?

Distance: Is the spot within 2 km of your registered residence?

The police usually check a map and may visit the site. If there is enough space on the land next to the unregistered building to park your car, they will issue the permit. They are not building inspectors; they won't typically check if the house on the property is registered or "illegal" unless it physically blocks the parking space.