Checkerboarding is a technique whereby a certain number of pixels are rendered in a checkerboard pattern, and then the ones that aren't rendered normally are inferred based on the information of the pixels surrounding them. Whatever your target resolution is, you render "half" that resolution, then cheaply render the rest (it's not strictly accurate, but it's "pretty good" by most accounts). Most PS4 Pro games render a 4k image using checkerboarding as a shortcut, which you might say is "2x1080p". A small handful of games are native 4k.
The PS4 pro in Mass Effect Andromeda is rendering 2x900p, and the checkerboard technique therefore produces a final image whose resolution is 1800p. Since it's supposed to be displaying in 4k, it then uses a conventional upscaling technique to produce the final 4k output to television. So to answer your question, no, it's not rendering in a lower resolution than the PS4 regular. 2x900p is a higher pixel count than 1x1080p. As to why you would render 900p->1800p instead of 1080p->4k, I can only speculate. I previously thought that the base PS4 was rendering 900p, in which case it made perfect sense. But if it's not, then I would have to assume that whatever rendering pipeline Andromeda is using must not be playing nice with checkerboarding. In some games on PS4, it is virtually "free", but it depends on the game in question and how it's set up technically speaking.