dyeing the epoxy is an intriguing idea. I would advise contacting MAS epoxies to ask them. alternately, you could contact interlux about the possibility of dyeing the varnish. since it’s organic-based, perhaps the addition of minwax oil stain would be compatible.
I think you’re right that if you dye/stain the wood before epoxying, then you sand or scuff the wood, it will be very difficult to touch it up and match the original dye job.
yes, there is variation in the color of the plywood veneer from piece to piece, but I thing that adds to the allure of the finished product. also, note that the interlux varnish has an orange hue so 4-5 coats of varnish will darken the wood somewhat. I am very pleased with the final appearance of mine after 5 coats of varnish.
ken