Here there is no question word to turn this into a question.
In that other sentence nuq is a question word, so nuq 'oH pongDaj'e' is a question asking for what should go in the place of nuq.
In this sentence, without the -'a' the sentence would be mara 'oH tlhIngan pong'e' which is a statement: "The Klingon's name is Mara." If we want to ask if that statement is true, then we append the -'a' to the verb and we get, mara 'oH'a' tlhIngan pong'e' "Is the Klingon's name Mara?"
The subject of the Klingon sentence is tlhIngan pong'e', while the subject of the accepted translation is the Klingon's name. While there is a case to be made that the subject of a Klingon sentence needn't necessarily be the same as the subject of an English sentence, this course only allows both sentences to have the same subject for "to be" sentences.
There is also a case to be made for this strategy. The Klingon sentence can be more fully translated as As for the Klingon's name, it is Mara. The sentence Is Mara the Klingon's name doesn't quite capture this emphasis of the Klingon subject.
For the same reason that "Is Mara the Klingon's name?" is not quite the same question as "Is the Klingon's name Mara?" Those two sentences are different in English and they are different in Klingon. Yes the difference is minimal and in most situations they could be used interchangeably, but none the less, they ARE different questions.