Spouse visa keep my passport option

Hi everyone, so my partner applied for spouse visa and attended biometrics on 4th July 2019. I submitted documents at vfs on 9th July. My partner paid extra fee to keep passport as she is lives in Afghanistan but applied through Pakistan Islamabad.

First question is the question regarding are you a national of the country you are applying from? I put no. I put her nationality as afghan and explained that she will apply for a visitor visa for Pakistan. This is due to visa centre being closed in Afghanistan and that the .gov site suggests all application going though Pakistan. Is this okay? I've realised on the application it states issuing office UK border agency Pakistan -Afghanistan

Second question, how does the visa work? When will they need her passport? Will it take a long time for them to stamp it or will it be instantly? So far it's been 40 working days and I have applied non priority as she had to keep passport to go back to Afghanistan.