It's difficult to mark really all artifact objects from within InDesign.
You could probably try to locate those objects in Acrobat and use Acrobat to mark these a artifacts. For complex pages/documents this could become challenging.
You might be more successful by using dedicated tools, like the Acrobat plug-in 'callas pdfaPilot' or the 'axesPDF QuickFix' tool which essentially have push button operations to mark everything that is not included in the tag tree as an artifact.
Thanks Olaf and "C".
Using the touch up reading order tool to mark the boxes as background hadn't worked. I tried that before posting my question. I ended up solving the problem by tagging them as "figures" and then entirely deleting them from the structure (I think any tag could have worked, they just needed to be tagged as something to be able to delete them from the structure). It seemed like a wacky work around but that's what I landed on by trial and error. Anyhow, PAC2 isn't red-flagging them now.