I agree Shutter, no FAA compliance was needed for those SEA covert ops, but the whole idea of 727 airdrop capability was the ability for civil airliners to covertly drop things/people on routine overflights of interesting or hostile areas. Countries that were at each other's throats often allowed overflights of civil aircraft. If you didn't have an STC, then that modified plane would be useless for normal commercial activity.
The US govt paid Pan Am big recurring fees to have their passenger 747s retrofitted with heavy reinforced cargo floors so that they could be used for military transport purposes should a need arise. Pan Am's capacity and range suffered from the extra weight and they were paid handsomely for this.
Might there have been airdrop capable 727s that served as normal airliners receiving a subsidy? Maybe no mods were needed and therefore no STC and no subsidy.
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The 747s you mentioned above were modified under a well known program in which other airlines participated as well. It was known as the Civil Air Reserve Fleet or some such thing. I don't know all the details but I think it all started long before the 747 and C-5 came along and probably involved the early 707s. But I think I can state with almost complete certainty that it did not involve the 727s.
Basically, the 707 prototype started the commercial jet age and the USAF bought a lot of KC-135 tanker aircraft to start off what became known as the 707. I think the USAF tankers were dimensionally similar to the 707 prototype (the "dash 80") but that the actual first 707s that went into civilian airline service were modified by increasing the cabin width in order to have 6 seats across plus some other modifications.
What became the civilian 747 was developed from Boeing's entry in the C-5 competition which was won by Lockheed.
If the SAT 727s were not involved in civilian revenue operations, then they probably would not require an STC. There are probably plenty of aircraft flying, especially those carrying outsize cargo, that have never been certificated by the FAA in the first place (that is, they are operating in the experimental category) or operating under some very limited authorization.
Robert99