Looks to me like the easiest way to have it working is to not use white as the base color of your polygons, but some other color. The color will be ignored anyway with your current RGB Matrix setup, and by not being white, you don't run intot he problem Joe describes of being ignored because it is the same color as the background.

Swarm of rats, half-decomposed/eaten corpses. Body parts.

This is the Delayed Drawn symbols that strikes. This features reapplies symbols after the effect pass to handle certain visual problems, but it only applies to non-building symbols (And with building symbols, I really mean symbols with built-in roof shading, like that tree also has)

Might be better to separate those into different sheets, but you can also fix it by disabling delayed drawn symbols, juts type DELAYDRAWSYM (enter) on the command line, and answer the prompt with 0 for disabled.

Note that this lasts the current CC3+ session, it is not a per-map setting.

Effects cannot be trimmed. You'll need to cover it up with something.

Personally, to prevent things from extending through a wall and into the "nothingness" behind, I like to use a mask that is made up from the background with holes punched in it for the dungeon (using a multipoly for that) and put that on top so it basically covers up everything outside the walls, including unnatural shadows.