Hi Andy, FrankL has it all correct. To answer your question: "Configuring those ports as output via the PDR is ok as long as my software does not "use"/change the ports' output?" Most MCUs have this issue with ADC pins near digital outputs switching during sampling/conversion. If you do run out of pins (for example in a lower pin count device) and must use some of these pins, use them on signals that can switch "when you want" (i.e. set a flag and switch them when a conversion/sampling is NOT in-process). Easy to do if you are using ISR for your ADC. Not so easy if you're using a timer to trigger and DMAC to get result. Good luck with your project.
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