If the projector is the one listed in your profile (Optoma HD131Xe), it looks like it does not have a mechanical lens shift mechanism - just a fixed vertical offset 'upward' of 116 degrees when projecting in tabletop mode. In that case for an elevated shelf mount you would need to flip it upside down as you described, and switch it to 'ceiling mode', to project downward to the screen. Your best image would result from mounting the projector level, at a height and throw distance that will give that 116 degree offset to your screen. Otherwise you would need to tilt the projector, and use keystone correction to square up the projected image.
Optoma makes a ceiling mount for the projector, and it should also fit many low cost universal mounts. You could most likely use a conventional ceiling mount inside your shelf unit as well, if the shelf location is a necessity and you wanted the extra adjustment flexibility - you'd just have to modify it for your application (e.g. resize the downtube that would be used for a conventional ceiling installation). Good luck!