Just FYI, TFE Paste is not a sealant. It's a lubricant and it's not designed to be used for machine threads like water pump bolts, it's only for mating pipe threads.
Tommy
There are all sorts of teflon pastes. Ones meant for mating pipe threads are indeed thread sealants for NPT type conical tapering threads (they're non-curing sealants that are not meant to fill the large gaps of parallel threads).
Now about your water pump bolts. Those don't have conical tapering threads. Also the threads don't form the seal. So no amount of any sort of paste on the threads will help with the seal. Be it teflon paste, or form-a-gasket (which I don't like on threads), etc.
Either the threaded hole is blind tapped and doesn't open into the water jacket, or there should be a sealing washer under the bolt head, or perhaps the blind hole is under an ear that projects outside of the gasket's sealing area in which case nothing is wet.
I like to use a teflon paste pipe dope on the wetted threads anyway, as it prevents seizing, and is less likely to wash out than a metallic anti-seize (which I would use on the dry threads in the third case I mentioned). Plus you shouldn't be introducing foreign metals (metallic anti-seize) into the antifreeze anyway.