I guess I would need more info --like what is the direct relation?
The direct connection is that he is also from Krypton. Plus, Jor-el sent him to Earth by mistake, after Thunderbolt switch the babies. Also he took Superman's name and wears his costume. It doesn't get more direct than that
I haven't read the JLA issues in question. Any other appearances, ever? Is he "floating around" or just a one-off (2-off)?
He never appeared again, but Crisis means he never will. Many characters that are in the Supermanica only appeared once or twice, but they still count and should count.
What are the compelling reasons that the canon rules need to be broken in this case?
He is another Superman in DC comics during the Sliver Age. The idea behind this project to to document all things Superman pre-crisis. Therefore that means that any and all Superman spin offs during this time should be included. The same case could be made for Ultraman of Earth-3 if he didn't appear in that one issue of DC Comics presents. Both were part of the Superman mythos that people still talk about to this day. Supermanica just would not be complete without the complete pre-crisis story, and that would include this Superman of Earth-A.