In a perfect world, the flange would set on top of the finished floor. In the real world, this often is not the case. Yours description indicates that your flange is just a tad lower, perhaps 1/8", than we would prefer, but it's still reasonably close. There are at least 2 ways this can be handled. First, you could use a waxless seal. These work very well and will make up the slight difference in height. The second way to to use a thick wax ring instead of the standard thickness ring. Do not use a ring with a plastic horn or funnel. I think 2 standard rings would be too much. As far as the caulk is concerned, my guess is that if you did have a leak, it would likely show on the ceiling below before you noticed anything from the back of the toilet, but leave the back open for your own peace of mind.