This is a great question actually and the answer is actually pretty simple.
You should definitely go with RGBA mode for anything but still limit yourself with your palette. Indexed mode could get you pretty often confused. For example adding another layer with a different sprite for reference would result in the sprite getting automatically recolored to your palette. In my opinion you should only use indexed mode if you need to make a retro game that will for example switch the palette during gameplay, otherwise it will be much easier for you to just stick with RGBA