I bothered me for a second. Then I stopped caring. Not because I didn't enjoy the issue, I loved the issue, because in the big picture of the Marvel U this series doesn't count.
I trust Rucka to come up with something satisfactory, but, all this means one thing: this Frank Castle is SMART. A genius level tactician. He figured out a way to hack in. Let's not forget he did have a helmet lying around for a while...
Again, in the large scheme of things, it's not like Frank will affect the rest of the Marvel U. You're not gonna read some issue of AVENGERS or IRON MAN and see in a bubble or thought caption: "I had to activate more security measures ever since Punisher broke in." or "I name this firewall the Punisher protocol".
Rucka wrote the smartest, craftiest 616 Frank Castle I can think of. I'm loving it and I'm sad to see it go.
I fully agree that Frank is a very intelligent soldier and tactician, and that he could likely infiltrate Avengers HQ.
But to even be remotely able to circumvent the safeguards that Tony builds into his armors nowadays and operate an Iron Man suit? A bit of a stretch.
Still you are right, this series likely will not "impact the MU for years to come" as Marvel is so fond of saying.