Yes, that is the commcenter patch. You would need to run it after every restart unless you install a startup script to change it on each boot.
I have unlimited and got one warning in April. I haven't seen a single claim from ANYONE that they had a 2 gig plan and got the warning.
I don't believe the VPN protects you. Which app were you using prior to your warning? I'm going to assume MyWi or pre-hide PDAnet.
I should mention - if you are using this for you primary net access, and using extremely high amounts of data (like, 50 gigs or something), I wouldn't be surprised if they are stretching their legal limits and taking a closer look at your usage. And honestly, at that point, I don't blame them, as that level of usage truly does decrease QOS for other users.