Based on anecdotal evidence, the answer is "it depends" - I entered twice in June using APEC and the card saved me a lot of time vs the foreigner line, but the e-gate would have had me through in seconds vs 5 minutes. However, there was a post in another thread where someone entered HND at the "wrong" hour and even with APEC were forced to wait behind the health check station, likely adding an hour or more to their clearance vs a few seconds with the e-gate.

So I think the correct answer is: what airports do you usually enter Japan from, and at what time of day.

I can also offer a personal example of an issue with APEC where an immigration inspector refused to accept a US card because it didn't have visa endorsements on the back. Unlike another poster with a similar issue, at least my inspector was willing to listen to an explanation of the differences between US/Canada and Asia issued cards and let me through.