In the new version, v1.92, you can't choose a transparency color in the export dialog when using PNG, unless you are using 16 colors (adaptive) or less. Even 16 colors dither & floyd don't work.
Edit: The same seems to hold true for GIF, TGA, and TIFF formats.
With BMP and PCX formats, the set transparent color button is enabled if you choose binary, but pressing it doesn't actually -do- anything.
Set transparent color in export, v1.92
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