To be honest, I was just saying that for comic effect. My main reason for using MonoGame is that it doesn't have a splash screen, and a secondary reason is that it's easier to create authentic-looking pixel graphics. I was just slightly annoyed that the old "pink = transparency" thing still exists.
Unity does have a visual shader editor, but last I remembered you had to use either the Lightweight or High-Definition Render Pipeline--and there was no way to switch once a project's been created.
Monogame has its strengths and weaknesses. If I were making a 3D game I would definitely rather use Unity, but there are certain things where MonoGame offers a lot more control at the expense of convenience. For example I can rebind controls in-game, a feature that isn't possible out of the box in Unity. MG being free as in free beer endears it to me as well.
To answer your question though, what I was trying to do was make a color replacement shader; i.e. any pink pixels are rendered as a unit's or player's team color. Once I realized what the pipeline tool was doing I got it working.
I suddenly got a lot of insight into how batching and draw calls work. My replacement shader worked fine when I only had one replacement color, but it didn't work when I had multiple "to" colors; the units on different sides would be rendered as the same color. Since I was using MonoGame's built-in sprite sorting, it was rendering everything in the same batch and not updating the shader information per-sprite.
I could render in immediate mode and do my own sprite sorting, but that would mean I don't get any benefits from batching. A better solution would be to create different batches for spites without a shader effect and sprites that do use one... But that means that sprites in the two different layers can't be sorted between each other, unless I add extra steps for compositing the two after they've been drawn. I'm already part of the way there by rendering to an internal render target and scaling it to match the window.
My creative energy was gone, but now that I've started learning things again I feel a lot better.