Is there any hardware butterflies that can attack physically isolated Unix/Linux machine in common usb drives, like VSC (Vendor Specific Commands)?
Any bug in the handling of USB devices can be exploited by malicious hardware. That's how the PS3 Jailbreak worked.
Remember that when you plug a "USB Flash drive" in a machine, you cannot be sure that what you plug is really "just a Flash drive". The machine sees it as a "USB device" which may claim to be a keyboard, a mouse, a network interface... A malicious Flash drive could be in fact a wireless network device, which claims to be some sort of ethernet card; the machine may react by automatically connecting to it (DHCP and so on): no more air gap !
Alternatively, the USB device may claim to be a USB-to-firewire converter and the device driver, already known to the machine, would then grant device-initiated DMA privileges: the device can then read and write any data byte in the machine.
Really, if you are serious about your security, don't plug untrusted device in a USB port.