Plugging screw holes before epoxy pour is, as you say, a recipe for disaster - meniscus around each plug needs removing at the very least. However, a sellotape patch over each tapped hole works fine, doesn't disturb the surface, and you can see where the holes are to drill a clearance hole in the epoxy when set. I had to have two goes at mine, and I had drilled and tapped the holes by the time of the second pour. I did have other issues, but tapped holes weren't one of them. In my case, the bow in the 1800mm X rails was around 3-4mm, and given 3mm wall thickness, machining or scraping were both out of the question!