That is the same thing I have been doing recently. When I place the pillars short like this I epoxy the pillars as a separate step before doing the glass bedding. I know that some guys do the bedding compound and then place the pillars short in a single step but I do not see any real benefit over the two step method except for the time savings..
When I did metal-on-metal pillars it was done in a single step. Metal-on-metal is nice looking but I currently like to leave them a tiny bit short.