Looking to purchase my first multi-family home (BRRRR), but have had a very unique situation with obtaining the CO. Has anyone come across this before? Is this "Special Permit" worth the additional headaches?

The seller and I agreed on a price for a 3 family home in upper NY and I then asked for a valid CO showing that it is a 3 family home since it is zoned in a 2-family residence.  The seller and town have been going back and forth for 3 months now to finalize the CO (the town saw it as a 2-family home but the Seller had some old documents pointing it to be a 3-family).  The town finally agreed to issue a "special permit" to legalize the building as a 3 family. The permit states it is a 3-family home but subject to: 

1) The town building department having the right to enter the premise with 24 hours notice 1x a year to ensure the home is in compliance with the town's codes

2) The special permit will expire after 7 years and a new permit has to obtained 

3) The special permit may be revoked if the owner violates any of the town's codes 

Is this "Special Permit" worth the additional headaches of the yearly inspections and 7 year renewals? 

Thanks in advance! Huge fan of BP.