Well you might be wrong, but EDI in general and HL7 specifically allow 3 levels of "fields in fields in field".

As long as your parser copes, and as long as you have appropriate structures to import into, its no big deal.

So now when I'm exporting data I need to know what nesting level it's going to live at so I can generate the correct separators?

I really think that might be the worst idea I've heard for a while!

It's not toooo bad :) But it's very much a "thing" in the real word. It's called EDI, and it's been around for a long time.

base64 encoded fields it is.

That was the right answer. You are hired!

Been there, done the Interop.

About 10 years ago, I worked at a place where we were embedding both XML and JSON in CSV fields.

Then there are always the people who can't generate a valid CSV due to escaping issues...

Nothing is ever simple.