Hi
kloppismydad,
some applicants have several university degrees, so they must upload one transcript for each. Some applicants have additional letters (of endorsement) that they would like to attach to their applications. The "Other Documents" section can be used for multiple purposes. For example, re-applicants can upload there a re-application essay.
In your case, if the letter from the NGO simply states that you are one their volunteers, you could upload it under "Other Documents" as evidence. But if the letter is to further endorse you, e.g. it is written by the President of the NGO to show his/her support of your candidacy, you could upload it under "Additional Letters".
Regarding letters of recommendation, there is no grace period. If your recommenders submit their letters past the deadline, you'll be considered for the following round.
I hope this helps.
Thank you
Alex