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It is true that the surface-matching feature struggles with donut-shaped zones. What you're describing (duplicate ceilings being created over these zones) is pretty typical from what I've experienced. You can correct this by manually deleting, intersecting, and matching surfaces, but if your work-around is automatically resulting in the desired surface matching and boundary conditions when you run the intersect and match measures, you've definitely landed on the more efficient solution.

I think, though, that E-Plus in general struggles with donut-shaped zones - not just from a matching perspective, but from radiation and heat-balance calculation perspectives as well. So even if you are able to appropriately set up zones of this shape, it's probably best to avoid them. I go as far as avoiding H- and C-shaped zones, when I can, as well. Not sure if this is just superstition or is actually prudent, but I just do it to avoid having to troubleshoot later. The image below shows how I'd divide the same zones - of course this does result in more zones than is explicitly necessary.