Looking at your John James McGinley's marriage record, I can't quite make out his dad's occupation, but wondered if it might be to do with the Army. Did you figure it out? Also, John gives his address as 16 Bonds Street at time of marriage.
Now, the house numbers on census aren't always accurate, but, if you look at house 16 in 1901, there is a McGinley family (and a boarder who is a Compositor - same job as your John James) with a widowed Margaret as head. One of the children is an Alfred. Looking at Alfred's birth certificate, his dad was a John McGinley, soldier. Margaret's maiden name was Taylor.
Whilst it could be a red herring, I think it is worth looking more closely into this family group, as potentially, they could be your John's family, albeit depending on how accurate Margaret's age is at 1901, as she is only showing as 38, and how accurate your John's is. Even if not his mother, there may be some link with John (for example, step mum). There is an adult male, James McGinley, born County Tyrone, also boarding in the household.
Edit: I've just realised from reading back on thread again, that you have probably already considered the above.