RailFanning is an art-form; RailFans are the paints - Ayush Kumar Singh

Even for HO quota, unless somebody is travelling on Duty Pass (which has a different quota), that person has to have a "PNR" which can be generated only at counter/internet booking. The PNR number is then given to the official known to the person who in turn passes it on, depending upon his ranking, giving his comments about necessity, and relationship with person requesting it. HO quota is then released by the final authority concerned, after compiling full list of requests for that train. Unlike earlier times, Paper tickets are no longer issued.
Quotas are spread all over the country: Some examples. HO includes Rashtrapati Bhavan, Rail Bhawan, Ministry of Defence, Parliament House (PH), local GM (Railway Zone/s) DRMs of different zones....
more...

and EQ (Emergency quota) with some individual stations including intermediate stations. All trains have a few berths kept vacant even after charting. For emergency travel either by officials or by passengers who have to prove immediate trvel necessity.
FYI, sometimes you will find Regret/WL1* indicating that no more booking permitted. But you may be surprised the next second when it shows Regret/WL2 or xxx.. This means a higher authority has asked for opening the Regret status to accommodate a VIP passenger/s to generate the PNR in order to allocate HO quota to him/her ! After that again it will show Regret/WL1* !!