There are some basics (at least in English) where it's generally agreed that a certain emphasis has a certain meaning. For instance, I think most English speakers would agree on the different meanings of "You went with him?" and "You went with him?" A straightforward written narrative should make it pretty clear which the reader should use.

I'm talking about odd fragmentary sentences which, by eye, convey a general feeling-meaning (about the characters internal state, for instance) but which really cause me to stumble in reading aloud because suddenly it's not clear how they should be spoken.

It's a style of writing that just was never intended for reading aloud. Not all writing is, and writing that's not is often VERY hard to podfic well.