While it can be debated whether the bike originally came with different frame number and engine number, there are a couple of other considerations.
What number is on the title? Engine number? Frame number?
Would you be titling the bike in the same state as it is currently titled? Out of state purchases usually require a serial number/VIN verification. This could cause some issues at the title bureau. Also if the bike is titled by the frame number, you would definitely NOT want to restamp a new frame tag with the engine number.
Does the gearbox number match one or the other?
I see the bike has had the front fender replaced with a Mk III one, so it possibly could have had some damage at one time. Could be the frame was replaced at some time with a used one. I would look closely at the rear loop for signs of weld. It is not unusual for this loop to be damaged in an accident and is fairly simple to replace. This could explain the wide loop.
The number issue, original or not, can cause some issues with a resale. More so if sold in a different state. Of course it in no way affects the quality of the motorcycle or the enjoyment factor. One of my favorite things about Commandos is that there is a good market for modified machines. They don't need to be (nor can they be) documented to exactly the way they came from the factory. In fact, many modifications make them more appealing.
Just my $0.02.