In HTML, I can have <table role=presentation> which indicates the table isn't a real table and is just used for layout purposes. This helps with screen reader navigation to real tables.
Is there a similar construct for tables in tagged PDF?
As far as I know, the <table> tag in PDF means it's a real table. I couldn't find any properties that would indicate otherwise.
Tag names in PDF are completely arbitrary. If you have access to the tags, just convert them to div or section tags. In Acrobat Pro you would do that in the tags panel.
The tags layer is only there for assistive technology, so changing it should not affect the look of the document, or anything else.
I would also check the ordering is ok, which you can do with the tags or ordering panels.
For automatically generated files, I would suggest the question needs to be: How do I layout blocks in a grid? (Rather than how to nullify a table.)