I’ve been away for a long time, and the issue with connected realms is very confusing, but I think my question is rather simple -
If I am on Bleeding Hollow, can I pvp with a friend on Agamaggan assuming we are the same faction?
From what I can gather Bleeding Hollow is not on the list of connected realms, but Agamaggan is. Does this impact my ability to play with my friend?
A connected realm is similar to a realm merge. It combines the population of multiple realms. The difference from a realm merge that you might have seen in other games is that the realm connection method allows each realm to maintain its identity. 
If you are RealID or BattleTag friends you can be in the same group on their realm and PvP, yes.
It isn’t a factor.
Here’s a Support Article we have on Cross Realm Parties:
Super informative. Thank you