But you do not have to create a Source/Citation that takes into account all possibilities. You create a S/C with the process you actually used. And if you use a second (or third) method they become their own S/C.
I can get many of the same records from Ancestry and FamilySearch. The S/C I add to the record depends on the method I used. In both cases it is usually a scan of the same record.
You mention the Register Office in Manchester. That the R/O may have some of its records stored by the central library or stored in a salt mine is irrelevant. To get the record you go to the R/O.
Gramps gives you the three components. Repository, Source and Citation each having various fields. Each user fills the fields so that another person has a possibility to find the exact same tidbit of information.
Remember, information put in the Repository does NOT get added to the S/C printed in reports. This is why I use the Repository to signify where I went to obtain the information.
You may find this thread of interest.