I am finishing a new shower, I used a pre-fab shower enclosure set and would like to tile the walls and ceiling over the shower in the long run. For now though, I'd like to wrap it up. I know I can prime and paint the backerboard but I don't know if this makes it unsuitable for tiling over later. Will I have to add a new layer of backerboard or strip the paint later?

I would suggest against painting the backer board, as I don't see stripping being successful and the magic of backer board relies on a modicum of absorption for adherence and bonding.

Thanks,
Json

The magic of backer board relies on a modicum of absorption for adherence and bonding.

I don't know if that is right , but it sounded really good!
Id advise not to paint the backer either, I really don't see how that will look very good,
As for the paint causeing problems with the tile being set, id say no. and here's why, we use a spray sealer once we install the backerboard which it is just like a paint , but it is just like having a rubber membrane, and the tile sets on that and the backer is totally sealed.
Now if the paint you use is laytex or glossy and can see a problem with that, the surface you set the tile on must be stable, that paint can't be peeling or looses in anyway