...why has it taken this long for anyone to notice that these satellite signals lasted for 4 extra hours after the last communication?
This is engine-status VHF ACARS we're talking about, right? Satellite monitoring of VHF traffic is well within the realm of the possible, but the job is finding the relevant ACARS blocks in what's likely a mountain of noisy signals intelligence data, not to mention getting it approved for release.
I'm not at all sure the overall scenario hangs together, but if you want to speculate about a functional airplane, a deliberate transponder shutdown, and a quick descent to below ground-based VHF and primary radar coverage, having a satellite notice the engines trying to phone home makes some sense, and would also explain why RR never knew about it.