The question is "after what?" Remember that "after" is also a preposition.
"The week after" is taken as a fixed phrase. So is "soon after". In both of your examples, we have a given time so we can understand these phrases to mean "after next week" and "soon after midday." In short, we are not repeating the time reference which would usually follow "after", so the meaning is clear.
Yes, you should have written "five minutes later", because "it rained five minutes after" makes me ask, "After what? Where's the time reference?" We have missing information.