It's always a fine line we have to try to walk on determining where to let grammatical variations slide and where to be a little more strict. In a classroom I would make those determinations on a student by student basis, but this software doesn't allow that. So we try to walk a middle line that allows some variation, but tries to maintain divisions between different grammatical points. Please continue to bring your concerns to these sentence discussions.
One of the things about the Klingon pronoun as "to be" is that it has a unique grammatical structure. The thing following the pronoun and marked with -'e' is additional information and not part of the core sentence. mara 'oH'a' means, "Is it Mara?" What is the "it"? That extra bit (pongDaj'e') fills in that detail and now we know, "As for her name, is it Mara?" (or "Is her name Mara?").
If the Klingon sentence were reversed and instead asked, pongDaj 'oH'a' mara'e', then pongDaj 'oH'a' would mean, "Is it her name?" And this time the "it" that is explained by that extra bit (mara'e') fills in that detail and now we know, "As for Mara, is it her name?" (or "Is Mara her name?").
Because there is a grammatical difference here (if not a semantic one), we have decided to be strict on this point and hope that it helps students to internalize that distinction. It won't work for everyone and I'm sorry if it was more frustrating than helpful for you specifically. But I hope this discussion has at least helped you to see the difference.
I disagree that the -'e' is extra information and not the core of the sentence. The -'e' marks the word as the topic of the sentence, what the sentence is all about. It is the most central part of the sentence.
It's the English sentence that's wishy-washy. Is Mara her name and Is her name Mara are virtually identical in meaning. The only difference between the two is that Is Mara her name presupposes that the name Mara is already under consideration, while Is her name Mara does not. Klingon does not make this distinction, so either English version is equally valid as a translation.
Duolingo has a bug wherein it is unable to display the hover-tips when the Klingon word begins with a glottal stop (the apostrophe).
'oH is a pronoun that means it. Adding -'a' to it in a "to be" sentence turns the sentence into a yes/no question.
mara 'oH pongDaj'e'.
Her name is Mara.
mara 'oH'a' pongDaj'e'?
Is her name Mara?