This is a strange sentence to include, I could understand all the words in it but had no idea what it meant. The concept of multiple Františeks makes sense but this could be a confusing sentence for learners.
I agree with you that it makes perfect literal sense. Unusual questions and questions about unusual situations can be good examples, as the learner has to stop and consider whether they understood correctly.
That would carry the implication of a regular repeating activity, such as “which F do you wait for on Tuesdays”. I don’t know enough Czech to know whether that would disqualify it in this case, but I am a highly educated native English speaker living in the UK so I know about the English!
That sounds to odd to not use the continuous tense here. That sure is possible but is also very unusual - as if one were waiting for a František every day, which is what the present simple tense in your sentence implies.
The sentence itself is quite absurd. But you can imagine that Frantisek didn't came from war so a woman still waits for him. In my opinion it makes equall sense as the sentence in present continuous (not very big) and moreover the aim of this exercises it to teach Czech not English so the sentence in present simple should be accepted.