I’m pretty sure it’s because of the settings. File → Export → glTF, then a dialog shows up and in the options tree you expand Data → Mesh → Vertex Colors. In there you have several options, which in my version are: Either don’t export the vertex color, or only export the active one, or only export it when it’s being used by a material. Then there’s two checkboxes: One exports all vertex colors even if not used by a material, but it says it changes something in a way I don’t understand. The other one exports the active vertex color when there’s no material.
I guess this in tandem with Material → Materials = Export/Placeholder/No export causes an unforeseen result in some combinations? Also, I have no idea what a vertex color being “active” means; I’ve never used or exported vertex colors…