Unity Pro 4.2.1fa, NGUI 3.0.0d:
Overrides don't matter, my project is currently Android and sensibly texture compression defaults to ETC1/RGBA16 but here's the thing, that's just the default and I can still override it per-texture and that's what I do because in some cases I want to retain true-color (ever seen a 16-bit compressed skybox? ugh) while in others I want to force RGBA16 compression:
When I do so and update the Atlas via Atlas Maker, my current texture import settings are overwritten by NGUIs Atlas Maker, whereas Unity Pro and Android Pro themselves always freely let me override/customize them wherever I please.
Now I get that Atlas Maker is re-generating the texture but it should be possible for it to retain texture import settings. Fine-tuning like this matters to me, and as I said the difference between a 21MB and a 10MB texture is no joke and as I keep updating the Atlas in this project for weeks or months to come I don't want to manually fix this up every single time...