How can I tell if katsuobushi is made from bonito or the real deal?
I suspect that what you have here is a translation issue:
There are a range of fish called &quot;Bonito&quot;, which are largely fish from the mackerel family. However, one of the fish also known as Bonito is the Skipjack Tuna (Katsuwonus pelamis), which goes under a range of names including Arctic Bonito, Bonito, Ocean Bonito (see the huge variety of local names listed according to the FAO here)
To quote the site:

UK : Bonito ,  Striped bellied bonito ,  Striped bellied tunny .
USA : Arctic bonito ,  Bonito ,  Mushmouth ,  Ocean bronito ,  Oeeanie bonito ,  Oeeanie skipjack ,  Skipjack ,  Skipjack tuna ,  Skippy ,  Striped bonito ,  Striped tuna ,  Victor fish ,  Watermelon ,  Hawaii: Aku ,  Aku kinai .

As food labeling requirements are reasonably strict in both the USA and Japan, I suspect that if you see it labeled as Skipjack in Japanese, then it almost certainly is Skipjack (well, so long as you can rely on the fisheries people to be properly identifying their species), and what you are seeing is just the local variant name which someone has decided is the name for this type of fish in the USA.