I've written several IEEE publications using lyx. They only accept .dvi (not pdf).
When I'm writing I use: settings/fonts/non-tex (all defaults) and settings/output/pdf(luatex) When I submit uncheck: settings/fonts/non-tex settings/output/dvi(luatex) The results look very different. The 2nd (submit) version has much heavier font, especially the title. Actually, I think it looks more readable. I have no idea why.