The progress bar is already not a part of the structure sprite, and the game does draw the rectangle above the structure. I don't know if calculating and rendering vertices is faster in this engine, maybe it is, but it's fine now. The rectangle function that I made uses a white pixel on the texture page that is already loaded, and stretches and recolours it to make a rectangle for things like the progress bar, so there are no swaps (basically works the same as the built in rectangle function, but without swapping pages). Drawing more sprites doesn't impact performance that much, so it's fine.
If I should optimize, it would be other parts of the code at this point. The crafters for instance start at the top of an array containing the recipes in the form of arrays of items, and check every one of those arrays against their inventory until they find an array whose items the inventory contains (and then they start the crafting countdown). This is really inefficient, and is probably having a much larger performance impact than the same structure drawing an additional sprite as a progress bar.
Conveyors do already use a shader to swap colours.
I hope I'm understanding your points properly, and not speaking past you. If you want you can add me on discord, it could be easier to talk there.