I think that knowing how Firaxis addressed serious bugs, not only they didn't bother to think about it, but we players didn't bother in the first place to bring their attention on it...
Maybe... they would even declare it a "feature"!
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No, I confirm that is impossible to carry someone else's units on your tranports, not even your Pactmates'.
You have to turn over the transport, and in addition to that you can only turn over ships inside friend's ports.
Then ther was a bug I discovered sometimes ago and reported in ACOL.
You can't even load YOUR units onto YOUR *empty* transport, if there's a pactmate's ship/air unit stacked with it. If it is already carrying some, then it works regularly.
I never cheked what happens if the above occurs in your or your pactmate's base.