Hi Alexey,
Sorry for taking so long to get back to you, and thank you for the suggestion, that worked great! I was actually able to avoid masking the turntable by using two different marker patterns under the object for each side, then aligning them in one chunk like you said. For anyone wondering, the rest of my procedure involved duplicating the chunk, aligning the two chunks (using camera based alignment, so that the two chunks could be merged later), removing half of the images from each chunk, building the dense cloud for each chunk, deleting the putty from the dense cloud for each chunk, and finally merging the two chunks. This results in one chunk with both sides of the object combined floating with nothing underneath it, which is exactly what I wanted.
Thanks again!