It seems to me that these simple past forms, with certain adverbs, such as "fós", can correspond to English present perfect (have/has + past participle) eg "Has she reached the college yet?", particularly in British English. This alternative is generally rejected in these exercises.
Such translations should certainly be allowed, since they are often the most natural option in English, as you say. 'Has she reached the college yet?' sounds much better to me than 'Did she reach the college yet?' If you report such oversights, they will probably be corrected.
"did she reach?" and "has she reached?" are two different tenses in English (the Simple Past and the Present Perfect).
The English Present Perfect is often translated into Irish using the Irish Simple Past tense (because, in most cases, there isn't much difference in actual meaning between the English Present Perfect and the English Simple Past), but there isn't usually any compelling reason to translate the Irish Simple Past into the English Present Perfect. I have no idea if a Present Perfect translation has been added as an acceptable alternative for this Past Tense exercise, but in most cases it would be OK.
The difference is that ar is the past tense interrogative particle, and an isn't.
All regular verbs use ar as the interrogative particle in the past tense. 5 of the irregular verbs use ar in the past tense, but 8 of the irregular verbs use an in the past tense - it's one of the things that makes them irregular.