Sorry, Abhay, but I am not Oesho. He will, no doubt, wish to add his reply when he sees your query.
All I can say is that I prefer to keep my coins under the actual ruler. What do I mean? I'm not always sure. When the State coins were first catalogued, all coins with the Mughal's name on them were catalogued as Mughal coins. Now we mostly try to put, say Nizam coins under Hyderabad state, Awadh coins under Awadh state and so on, taking account of the date on which the state became independent. This is also true for states and mints taken over by the Marathas - we usually cataogue them as Maratha. Ditto BEIC. The Governorships under Mughal Emperors are a slightly different story - in theory the ruler remained the Emperor. Some emperors ruled in full power, others were more like figureheads, even puppets. It seems to be a matter of discussion, in some cases, whether the emperor had or did not have actual ruling power over the places with Mughal governors, and this changed from time to time.
In short, I think it is a matter of personal choice. I know an eminent numismatist who keeps all his coins stored under the mint of issue, in alphabetical order of mints irrespective of independence or area where the mint was located, which shows the development of the coins of that place in a very useful way. Most of us keep the state coins separate from the Mughal coins, but so often exact independence dates are a bit fuzzy. And what do we do, for instance, with the few Rohilla coins struck during temporary occupation by Mughal / Maratha armies that were soon gone again? It perhaps depends on our view of history and how we see the sovereinty of later Mughals, some of whom ruled, in the true sense, very little more than the Red Fort and a bit of Khalsa land.
I don't think it is sensible to try to lay down rules about this sort of thing, except that the way we store our coins, and list them, must suit our own view of history, rulership and the way we study the coins against their historical background - and that will vary from collector to collector. Nobody is wrong, and everybody is right. Win - Win! How often does that happen?!
I will also be very intereted to read Oesho's views, as I know he has thought about the matter deeply, and may have reached firm conclusions that will assist us all to get this complicated matter straight in our minds.
Salvete