From beatlescollecting.com seems to confirm that Capitol was sent all the masters, including all the different mixes, from which they were then free to choose. I suspect the longer ICI was made in the UK, not spliced together by the US:
"All of the songs on the mono version of the album are true mono mixes; however, four of the songs, "I'll Cry Instead," "And I Love Her," "Any Time At All" and "When I Get Home," have mixes different than those appearing on the mono Parlophone A Hard Day's Night LP. These unique U.S. mixes were prepared by George Martin. "I'll Cry Instead" is an edit of two takes. The mono version appearing on the Capitol album has an extra verse not present on the stereo mix or the U.K. mono mix. The mono album was mastered by Billy Smith on June 29, 1964."
"Ten of the twelve songs on [Rubber Soul] are from the British album of the same title. Except as noted below, Capitol used the same stereo mixes as those on the British album. Capitol used the November 11, 1965 mix of "The Word" rather than the later November 15 mix found on the British LP. Also of note is the false start guitar intro to "I'm Looking Through You" that is present only (at least until 2006) on the stereo Capitol album."