> The same applies to other tools. Again, every effect is doable now, 
> but the UI would be much cleaner with the notion "colors", 
> not "color, and oh that extra transparency channel" so it is treated 
> like something alien among colors (in nature it is not -- water, 
> glass, air are transparent as well as the chalk, snow, paper are 
> white).

And nature hasn't CTRL+Z. There are things that we must live with.
Gimp is a computer program. It -like others- may or may not reproduce
natural certain behaviors of natural media, because it's a computer
program and there's code behind the tools you use.
Maybe you'd like to point us a program that already has that feature so
we can see what do you actually mean with "transparent color".
As other people pointed out, what you're asking for seems quite similar
to the substract mode, that is already available both as a layer
blending mode and a blending mode for the brush and airbrush tools.
And the alpha channel handling is quite the same that other programas
have (like the acclaimed Adobe Photoshop).
Could you please try to explain in a more accurate way what do you need?
As far as I could undestand, it looks like you want to paint with air,
wich sounds pretty funny.

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