I had a 1971 Cuda that I bought from a classic car dealer in Michigan back in 1995. The idiot dealer wrote the vin number incorrectly when issuing the title and the state issued me a title with one additional number in it. Moved to Florida in 1998, and when I went to register it, because I had put the car up for sale, Florida immediately told me it was an incorrect vin number. I contacted the dealer in MI and they told me to send them the title and they would fix it. Well a guy showed up to buy the car and he wanted it now, said he would deal with the title. Sold the guy the car, and he went to the DMV, and they sent him to the police to check the vin's on the car. Well, they found out that the car had 3 different vin numbers, none stolen thankfully, but none the less it had 3 vin numbers. The police said that the car was a 1970 and not a 1971. They ended up issuing the guy a state vin number.
Back in the 1990's when people were restoring these cars, there were no replacement body panels, like we have today. So, if you needed sheet metal, you just went to a junkyard and cut off what you needed and welded it onto your car. Apparently, when this car was restored, they cut pieces off the front of one Cuda, and the rear of another and welded them to this car. So, one of the hidden vin numbers in the front was from one car, the one from the rear was from another car and the dash was from a third car... So, it does not have to be a stolen car, pieces could have come from multiple cars.
Only hidden vin numbers in Mustangs that I am aware of are the ones under the fenders, and those can easily have been removed or altered. How many cars have you seen that the fender aprons have been replaced on? A lot, and I can assure you those vin numbers were never put back on.
These old cars were so easy to steal and change vin number on that it is a joke. You will still see people selling titles with the dash vin on eBay all the time for rare cars.