Tiled has per-layer tinting, which could be used just as effectively. I'm not familiar with other generic editors. Tinting a quad is one of the easiest things to do, so I suspect the reason per-tile tinting isn't common is because it'd require annoying GUI work, and isn't commonly needed.
Another approach could be to make hue, saturation and brightness changes via a shader in your prefered Game Engine or manually in Photoshop via the HSL layer.
eg. https://www.reddit.com/r/godot/comments/tyji8r/seeking_an_hue_shift_shader_with_...