Please remember, there was never a Capitol Records release of A Hard Day's Night soundtrack. United Artists had the rights, at least in the U.S. So whatever EMI/Parlophone sent to UA, must have been part of a contractual agreement. Perhaps the Beatles had to agree to a minimum or maximum song length for the soundtrack. Originally, UA had the exclusive rights to all original songs submitted for the film, including "I'll Cry Instead". In an unusual spirit of generosity, Capitol allowed UA to include "Can't Buy Me Love" in the soundtrack, even though Capitol had already released it as a single. When ICI was not included in the film, the rights reverted back to Capitol.
Now for the big question: Did Capitol receive the master tapes from EMI or UA? That might explain a lot.