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Getting air out of #3 spark plug when you pressurize #5 seems impossible, unless #5 intake valve is leaking real bad and #3 intake valve is open at the same time that #5 is at TDC compression. That might let air into the intake manifold, up to a closed throttle and back down the intake manifold to the other cylinder. As far as air leaking out past the piston and back up through another piston wouldn't be possible unless the crankcase breather tube is completely plugged.
I agree that if you position the cylinder so both pushrods can be turned would pretty much confirm that both valve on that cylinder are closed, which is the way you should be testing.
The way the crank throws are arranged, #1 and #6 are both at TDC, one on compression and the other on exhaust/intake (with both valves possibly open at the same time). Cylinders #2 and #5 are paired, as are Cylinders #3 and #4.