Just draw it tight enough to bring the flange into the caulking so that there is a seal. This may allow the thicker layer of caulking to flex without breaking the seal. Then again, it may not. Even on well built boats, as they age time will break the caulking seals around ports. For hull sides that are fairly solid, you can use the same method as for window frames described above.
Most people find that sealing chain plates that go down through decks to be impossible.
Between the flexing decks and the stress on the plates, it really is. Silicone and other types of caulking won't work because it won't stick to stainless steel and its impossible to get a water tight seal. To make matters worse, if the chain plate is bolted to a plywood bulkhead, the leaking is going to cause the plywood to rot and eventually the rig will topple over. The answer to this problem is to design a method that limits the amount of water that can enter. First of all, remember that when it rains, water is going to run down the rigging.