+1 on the InDesign rant.
I solve that problem in ID before exporting, by, for example, searching for all italic character strings and applying an appropriate named character style to them. Repeat for bold, etc. as needed. Then select the entire document and "clear all overrides."
Follow up with a severe lecture to whoever created the ID file in the first place, requesting that they never use local formatting overrides. They'll probably make YOU the new internal book designer.