I've tested a few themes to see how they affect the standard notification area icons (as in, not using Ayatana Indicators). As you can see in the image, themes like TraditionalOK and Ceres render these icons at the correct size. However, Ambiant-MATE and Mint-Y render them oversized. This was all tested with a 28px panel.
I suspect Ambiant-MATE and Mint-Y render them incorrectly because the themes were designed to use different status icons (Ayatana and XAppStatusIcon, respectively).
Does anyone have advice on how to modify those themes, so they render the standard notification icons correctly?