You have to educate your clients to use only Acrobat to view PDFs as all other viewers have a problem to show many PDFs correctly. That is how it is. You cannot change the world. Even if you decide to send flattened PDFs without the live transparency you will get claims, depending on the used viewer, about lines, frames, missing fonts and wrong colors. There exists no PDF which shows up correctly in every PDF viewer except with Acrobat.
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