I think Timbermate filler has been used successfully on neck joint issues like yours, as long as it is completely dry before painting. Would be curious what you have heard TD? I know that sometimes a water based finish can re-activate water-based products that it goes over, but I had not hear that about Timbermate?

Whatever the risk I don't think I would use epoxy around the neck joint. One of the reasons for using a water-based glue and water-based filler around the gap is so that you could get the neck off with some steam or heat if you ever needed to reset or replace it.