Hello Danc, nice work on tyrian, it's one of the few great-looking top-down shooters for the PC. Lots of tilesets in it, too. Much much work.
About your question, on top of what Alex said where anything using millions of colors is probably painted, we usually refer to some tools, even in indexed color paint programs like Dpaint or Brilliance, as 'dirty' tools. Dirty as in 'unclean' not as in 'bad', where the result is fast to make, but undermines the pixel-art-type of detail that we usually like to see. Using shade modes (or darken or other similar ones) is borderline (if Brilliance is anything like Dpaint and Pro Motion), really, it can get kinda dirty as a tool because lots of passes to a lot of area can be applied pretty rapidly as you said, and the attention to pixel-level detail can be weakened. Mainly though automatic AA and Smear mode brushes are the main offenders when it comes to 'dirty' pixel art. For example, a lot of the demoscene art from the Amiga days that I'm sure you're familiar with would more likely constitute as
index painting than pixel art. Most of the time, it's indexed painting with a reasonable amount of repixelling on top. Some artists are more of pixellers, some more of painters. For example, Danny is a painter, Made is in-between, and Cyclone is more of a pixeller. Danny practically used Dpaint like Photoshop. A lot has to do with palette control and using every shade to it's maximum effect. If you find yourself making 16 color ramps of one hue, you're probably about to index paint

I was reading your blog and you seem very erudite and intelligent, not to mention passionate about your interests. Would you be interested, since you're around, to have a thorough talk about your process when it comes to pixel art, and answer the questions of the users of Pixelopolis on the subject? Kind like a Commercial Artist Q&A?