The idea of using a separate transparency map is a bit of a throwback to an earlier era, where we would use black-and-white bitmaps as transparency masks to draw sprites.
That said, it's still a perfectly viable technique today. There's really no appreciable performance difference between using a color and alpha map versus one color map containing alpha as an additional color component. There may be some minor issues regarding disk or memory footprint, but those will mostly be irrelevant in the grand scheme of things.
A good reason to use separate image sources like this today is not for game runtime performance but authoring performance. If you only have tools available to you that don't work well with images containing alpha channels, or you simply prefer to work this way, it can be more efficient for you to do so rather than in a context where the alpha is embedded into the color.
Similarly if you've chosen a particular image format that doesn't support embedded alpha channels for other important reasons, you may end up using this "separate mask image" technique.