Fortunately, we are our own service provider and plate jobs directly with our own equipment. Using PDF/X-4 has recently become another standard we use, but most of our previous output settings were based on "flattening", although I think we could adapt all jobs to PDF/X-4 (a custom setting to keep raster resolution, etc.) but as I am self-trained and have not dealt with very many jobs using transparency overprinting. I also do not know definitively if there are any pitfalls I should be watching for using this setting across all of our output.
It seems that using opacity and the occasional "double-object" placing a white one under the colored is indeed a suitable work-around. It is nice to have such good software available without having to deal with Adobe's subscription or Quark's annual upgrades, however it is easier to break the Illustrator dependency than Quark's. I did purchase Designer & Publisher last year, along with using the GIMP & Inkscape (for outlining raster mostly) I have a workflow that is exciting to move forward with, and the occasional hiccup is fine with good gentleman as yourselves to help us beginners move along. Thanks you and May the Force be with you!