I use the 90mm macro on my 6500, and have occasionally lost shots when the auto focus got confused - which I suspect was because of particles in the water. You have to remember to check that the lens' focus ring is set to auto before closing the housing, or you'll be stuck with manual focus and not able to reset it via the camera's menu once you're underwater. And you also need to make the right selection on the focus range switch. But the AF-C works really well with mobile subjects. I don't bother with the IBIS.
That's interesting about the close proximity of the buttons making them difficult to use. Given the compact size of the Sony ILCEs, it's always going to be a challenge for the housing designers to keep the buttons apart - best example is the cruciform group to operate the main control wheel - they must be pretty awkward in drysuit gloves too. On the NEX6 housing, the AEL button is also next to the video control, and using the 3-click trick to switch from AF to MF and back on the NEX6, I've never hit the video by mistake: from the pictures of the a6000 housing, the position looks very similar, so I wouldn't anticipate an issue.
But then, I'm a confirmed warm-water diver ... and you're an Olympus user.