Reference points in InDesign are essentially the same as they are in Illustrator… Nine points forming a box with a center point around whatever path you have selected. These points allow you to stretch or resize an image box.
If you enlarge an image in InDesign by scaling then you will notice it expands your image box from a default point that stays consistent throughout your images. Mine is set for the upper left point which works well when I’m expanding an image to fill a given space in a document.
If you want to change this, simply select the image with your Selection tool and in the upper left corner of the Selection tools menu is that familiar diagram with nine little points in it. Highlight one of these to change the Reference point. Simple as that!
The Reference point stays the same no matter what image you are using in that document.