I have never heard that the stones are elsewhere. What I have heard is that certainly at the time William was buried, there were often no stones used, so there may be nothing to find. Also, the chances of finding a readable stone from that period are slim.
More importantly, you say you have the other 9 stones. Does this mean you found Thomas' stone???? Or his wife's? That would be a find! A cousin & I have been doing extensive research on the Framptons but other than an often-quoted date, we have found little on Thomas.
Do you also then have John & wife/family? John seems to fall into a black hole at a young age and resurface in PA. Would be very interested in seeing your photos & willing to share what I have.