For an app with multiple values of a color with different opacities, is there a way to identify the swatch being used by naming?
There's no way currently to name your color favorites/swatches. Please upvote this feature request to help raise its priority: Name color favorites/swatches – Adobe XD Feedback.
In terms of the same color with differing opacity, though -- the swatches do show a checkerboard background, which should make big differences in opacity easily noticeable. You can also see the precise alpha value by hovering over a swatch:
Hope that helps!