Basically it's a matter of grammar rather than nuance.
As you may know, in is (semantically almost bleached out but still functioning) topic marker in the theme-rheme structure of Japanese. In other words, it delimits theme and rheme parts of a clause. And one clause may only contain up to one theme and rheme respectively.
Then, what happens if you use two at once in a sentence?
>
You may feel a sense of dissonance because:
* [ [ ] ]
* [ [ ] ]
It has two possible breakdowns so you can't decide which is the main theme of the sentence.
(Note that some people don't feel anything wrong because they conceive to be a monolithic chunk.)
Thus carefully written sentences often omit the in in order to avoid confusing readers by any chance.
* ****
* ****
Of course, in the colloquial language, has taken over them so that the difference between and is neutralized.