Chances are, if a shop has a nitrogen generator, they aren't going to use regular air instead. They don't make enough money off the nitrogen to use it as a scam. But, true enough, just like the oil, you don't really know for sure unless you do it yourself and you know that the generator is working properly.
The way the generator works is, it sucks regular air into filters that designed to let the smaller oxygen molecules pass on through and captures the larger nitrogen molecules.
When they fill your tires, it'll contain somewhere between 93-98% nitrogen. Anything in that range offers the same results, with about 95% or 96% being optimal. If you need to top off and thus reduce the percentage to 90%, that's not enough to make any significant impact on the benefits of nitrogen.
Incidentally, if you had 100% nitrogen in the tires, the reverse would happen in that oxygen would start leaking into the tires. And it would continue until the nitrogen in the tires was somewhere between 95-96%. Apparently that's the perfect balance. Or something.
Slow and steady, even in expediting, wins the race - Aesop