It looks like this tool has its own hardcoded font for displaying all of the text, and when I fed it my usual 9x16 font it was very difficult to read.
An option to configure the palette (or, better yet, read the palette from Dwarf Fortress's own configuration files) would also be nice.
Due to the possibility to use ttf-fonts in the game now tilesets without characters may be possible. Thus another tileset is currently used for text. Edit 'config.txt' and copy the path value from '[TILESET:...]' to '[CHARSET:...], then the letters of your tileset will be used.
You can also use a custom palette. Copy your 'colors.txt' file to the application folder and rename it to 'init.txt' (older versions had the color settings in init.txt, as you probably know, this was not updated yet).
There's some other oddities as well with the tree types - notably, the underground trees show a bunch of square block tiles to the right which are presumably meant to be the "dead", "sapling", and "dead sapling" tiles not being defaulted properly to 198/231/231 (╞/τ/τ).
Have a look at the 'Token' string in the lower portion of the interface, this will tell you which token your are currently editing. The boxes are used to represent color values (e.g. 'DEAD_TREE_COLOR'). The smaller square is foreground color, sorrounded by the background color. If 'DEAD_TREE_TILE' for the object is defined for the plant its tile will be shown instead. They are missing in the raw files for underground trees (except for blood thorne), so only the color can be changed.
Mined stones aren't being shown in the proper color - they should use the material's BASIC_COLOR.
As the 'TILE' and 'ITEM_SYMBOL' use the same color and the color can already be edited for the 'TILE' value, there is no color shown for the 'ITEM_SYMBOL'. Otherwise two different color values might be selected by the user for the same 'DISPLAY_COLOR' token of the mineral.
Which object tokens are shown in the application and which color tokens are associated with them is defined in the 'definitions.txt' file. You could replace [TILEDATA:ITEM_SYMBOL:] with [TILEDATA:ITEM_SYMBOL:DISPLAY_COLOR] if you prefer that. In this case the color values associated with the symbol will be saved as DISPLAY_COLOR token.
Glowing eyes (goblin, kobold, and blizzard man) are similarly missing their colors (specified via GLOWCOLOR).
I did not know that. You can resolve this by opening 'definitions.txt' and replacing [TILEDATA:GLOWTILE:] with [TILEDATA:GLOWTILE:GLOWCOLOR], then.
Have another begging urging plead from me too.
ttf Text and custom color palette would be awesome.
I don't plan to add ttf-support for now, sorry Ironhand. There are lots of applications that allow you to have a look at your font.
You can already change the color palette (see above) - you'll probably still have an old init.txt with your color settings, you might just copy that to the application folder. Unless you meant the color of text elements, these are still hardcoded. As I'm currently far away from the computer with the source code, I can't change anything about it, sorry.