Well, there’s a feature Table > Convert Text to Table. So I assume that would be pretty easy to script.

Are you saying you’re exporting IDML from the database? If so, the database could probably spit out the correct IDML to make it a table already?

Does the Links panel show what page it’s on?

If you export as IDML and then open the IDML does it go away?

Yes, you can keep files as native files, such as PSD and AI.
I strongly recommend NOT converting to CMYK (have written about that extensively, such as this article).

Yes, I understand. But if that highlights everything in blue, then it means that you have local formatting (formatting on top of the paragraph style) everywhere. So one solution is to change the font and size of the text until it matches the paragraph style. Or, maybe easier, change the paragraph style definition to match the current text.

For example, if the main text is Times Roman 12 point, then change the Basic Paragraph Style to match that. Then the blue highlighting should go away for everything except the differences