Just as in the regular racing rules, AC rule 18 applies when "...at least one of them is in the zone".
Unlike the regular racing rules, AC rule 18 does apply between boats on opposite tacks on a beat to windward. The definition of overlap is different too, so the boats were overlapped.
Therefore, JPN was obligated to give SWE "mark-room", even if she never entered the zone (which is 3 boat-lengths from the mark) herself.
The AC rules, however, define "mark-room" as "room for a yacht to sail her proper course to round or pass the mark on the required side. If room includes a change of tack, such tack or gybe shall be done no quicker than a tack or gybe to sail her proper course."
(1) Even though rule 18.3 does not apply at a gate mark, JPN only needed to give SWE enough room to sail her proper course, and
(2) JPN could not force SWE to tack quicker than she would to sail her proper course.
I think the umpires called a penalty on JPN because SWE had to tack more quickly than she would have in the absence of JPN (and therefore JPN did not give SWE mark-room).
Both the penalty on SWE in her race against NZL, and the penalty on JPN vs. SWE could have been avoided had the outside boat sailed a little wider around the mark. In both cases, the penalty decided (most likely changed) the outcome of the race.
Match racing is supposed to be aggressive and close boat-on-boat maneuvering, but getting a bit too aggressive, and too close can be catastrophic.