as these left buttons here are meant for normal selection, and are not meant to be affected by the species colour:

This was likely unintentionally changed when we updated to Godot 4.

Some analysis by Athriq:

Regarding that menu, the left buttons shouldn't have different hues (at least not what the original GUI design intended). Looking at the menu's code, maybe this line have something to do with:
CustomDropDown.cs
181 Popup.SetItemIconModulate(index, item.Color);