1. He will come back in five days.

1-2. He will come back at the end of five days.

2. He will come back within five days.

3. He will come back after five days.

4. He came back after five days.
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Does #1 mean #1-1?
What about #3? I think #4 is right.

3 answers

#2 means any time before five days has elapsed (could be one, three, five days - WITHIN five). At the end of five days means just that - five days will pass before he returns. In this case, "in" and "within" can be taken to mean something different. "In" means the whole five days. "After five days" means SOME TIME after five days have elapsed. Maybe the sixth day, the end of the fifth day, the seventh day? It implies that five is the minimum he will be away. Really, "in a day" implies the whole day while "within" means a part of the day in your earlier examples.
Can we use #3?
In the past tense, we can use 'after' as in #4? What about #3 in the future tense?
#s 3 and 4 are correct as they are written.