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It's mostly because of American airline companies being weird with sports equipment, and if you can fit the bike in a normal sized bag that will go in the hold then it counts as normal luggage.
This is the theory.
Except I have S&S couplers and I can tell you the theory does not work.
The S&S bike cases have no space for shoes, tools, bike clothing, helmet... let alone normal clothing, toiletries, etc.
So you are still going to have to check-in another bag (can't carry tools on, etc) and you're not saving anything in fees.
Also... bikes in boxes with other stuff jammed in tend to weigh quite a bit and still be large, so you're on the cusp of excess baggage anyway, especially for cheaper internal flights.
My solution for my Seven: No S&S, just get a proper sized bike box/bag.
S&S are not really worth it.
That said, at least they have zero impact on frame stiffness, etc. If you've got them your ride isn't affected by them.
FWIW I don't understand why S+S is a thing when there are readily available carrying cases for normal bikes.
Please educate me.