I'm a big fan of your stone symbols, I've included in my tileset many of the mineral tiles from your Loyalist tileset.
I don't know if it's what you were looking for, but these are my observations about your tileset (both as a user and tileset creator):
Purely decorative stones and layer stones are redundant. I've considered dropping the layer symbols altogether and just go for one symbol for 'useless' stone. The only thing that stopped me was the glooming oppression of 50 levels of identical monotonous stones.
Talking about the Loyalist tileset specifically, the greatest part of your design is the small stone symbol used above the layer symbols. It's both a clear indicator of a stone, clear indicator that it's mostly worthless, and a clear indicator of the foreground color of that stone. That's really good.
The layer symbols are individually nice, but they don't look so great when tiled in large number.
My suggestion: Combine the Overhaul tileset's layer background with the Loyalist tileset's stone symbol. That could give you a chance to reuse those good stone backgrounds.
For metal ores and gems, either sets are great, except for the background in the Loyalist's, that could use some improvement.
I've found that, using PNG's alpha transparency, simply using a flat 50% opacity white background (resulting in a 50% foreground & 50% background color bend) was already a good improvement. It made everything look crisp, and was very easy on the eyes.
For the special ores.
Non-Unique ores (Iron, Fuel, Flux, Gypsum), those really deserve their own tiles, and those tiles are great already. Probably best not to mess with them.
Unique ores (Adamantine, Bauxite, Kimberlite & Obsidian). While them having an individually unique tile is nice, it's not really necessary. You can save tiles by having them all share the same graphic. Color coding and the users' eagerness to know the value and use of special ore should be enough to distinguish them.
That's my 2 cents.