I had wondered the same thing. Since wax hasn't stood the test of time, why not use some more modern material? Nobody coats flybacks with wax nowadays.
I once re-coated a flyback with RTV, and in that discussion Eric H. suggested this stuff as a better material, since the thin liquid can seep down into windings:
http://www.aervoe.com/paints_coating...y-Coating.html
The fly that I did with RTV eventually failed, and I replaced it with a NOS transformer from Moyer's. The new fly was a correct replacement, but it had a plastic raincoat over the winding, rather than wax as on the original. Apparently, even in the few years since manufacturing the original and the replacement, someone had decided that wax was not the best solution:
Just my $0.02.
Phil Nelson