(And Panetta misspoke a bit about the plane being built in "another country". It was built by Boeing in the US. The interiors, however, were installed in another country. Minor point. But, still.)
Aircraft procured for presidential use are monitored throughout the entire manufacturing process, or are thoroughly inspected to the point of nearly being disassembled before they're certified for use by POTUS. Most of the lifetime of the Qatari 747 so far has been spent outside of this monitoring window. So, nothing can be trusted. Most of a presidential aircraft is essentially a SCIF for open discussion of sensitive topics.
Behind the panels and under the floors are wiring bundles so numerous and complex, anything could be hidden in there - bugging devices, cutters, poisons, acids, communications, anything. It would be impossible to properly inspect all of it without removing it all and going through it strand by strand. Did they do that?
Every electronic box in the plane - from avionics to the panels that operate ovens - could have circuitry in them, right down to the circuit board - or even chip - level, that could be used to monitor, commandeer or disable that device or the whole aircraft. There are hundreds of boxes in the plane. Did they remove every one and test them?
There could be secret fuel cut-off valves installed in the engines that could be remotely actuated.
Did they inspect every cubic inch of the fuel tanks? Could be explosives in there. Or capsules of corrosive agents that could release over time and eat the fuel tank walls or contaminate the fuel at random times causing engines to malfuntion over the Atlantic.
Tracking devices can be as small as a sugar cube. Have they inspected every interior volume - the wings, the vertical stabilizer, the engine nacelles - for the presence of questionable or unknown devices? This is a true needle in a haystack.
Has the plane been swept for radioactive materials? Pellets of - or even dust treated with - polonium could be placed anywhere to gradually drag down the health of anyone on the plane.
The Qatari AF1 is a literal Trojan Horse. The military was stupid for even considering letting US leaders fly on the plane. I'm surprised they could find legit military pilots willing to fly it.
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