The lesson is not very clear about this, but it does point you in the right direction. Here is the relevant section from the lesson:

When the main verb is in Le Présent Indicatif, après que is followed by Le Présent Indicatif to express a habit (after they come, they [usually] do that) or by Le Passé Composé when the action happens BEFORE the moment it is being reported (He goes after I've done it).

Unfortunately, there is not a single example provided which would demonstrate this. (@note to kwiziq team: I think that one or two examples would be helpful here.)

Je prends mon petit-déjeuner après que tu te lèves. -- I (usually) have breakfast after you get up.
The present tense in the après clause makes it clear that this is a general statement.

Je prends mon petit-déjeuner apès tu t'es levé. -- I take my breakfast after you get up.
This is a one time thing. In English, using the future tense in the first clause would be more natural and underline the temporal structure: I'll have my breakfast after you get up.

I'm sorry I still don't understand this. Chris offers 'tu t'es levé. -- I take my breakfast after you get up.' That's wrong. Tu t'es leves means 'you got up'. Not 'after you get up'. Surely that is what the problem is? It could mean ' you have got up', but in English in this context that is short for ' you will have got up' .

Well, I'm still baffled by this. There must be something wrong with the English translations - I find it hard to believe anyone would ever say: "I am having breakfast after you've gotten up." 

Could you explain the sequence of events here, and at what point it would be said?

P.S. According to the following links, when the main clause is in the present, the subordinate clause has to be in the passé composé, but this always indicates a repeated event.

https://bdl.oqlf.gouv.qc.ca/bdl/gabarit_bdl.asp?id=1132

http://parler-francais.eklablog.com/apres-que-indicatif-a3704329

I think the original question/answer that Julian queried, was in fact correct. The sequence of tenses in English is just different. 

The following example is also given in the lesson, and it's very similar to the one given by BDL, so it must be a repeated event.

"Après qu’ils sont arrivés, ils vont saluer ma mère." = "After they've arrived, they go and say hello to my mother."

It's just the explanation in the lesson that seems to me to be wrong.