This done to enhance light gathering, right? Normal color CCDs have per-pixel filters so lose some light in order to gather the light at the same time?

  The most common method is to blanket the CCD pixel array with an alternating mask of red, green, and blue (RGB) microlens filters arranged in a specific pattern, usually the Bayer mosaic pattern. 

If you apply some sort of Bayer filtering, you are reducing the number of pixels per channel that the sensor can take. If you use all of the pixels for each channel, there is more information in each channel. The trade off is that you have to take multiple full sensor images vs a single image. It also gives you flexibility in what filters you want to use as full sensor filters are interchangeably. High-end telescopes can use filter wheels which can hold multiple filters like Hydrogen-beta, OIII, etc, and swap out very easily with some controllable from software.