Assuming that the Murphy and Carmichael, that are hanging out if Chicago between, are the same two from the real world, they have indeed turned out to be special. They got positions at Ark Angel PD in Chicago between.
Probably because of the nature of their deaths, more than that they'd been empowered in some way in life.
I don't think that Malcolm has to be special. But it isn't that he couldn't be. Eb describes him as exceptional, hell near angelic, unless you read that differently than I do. But putting that aside.
Let's define terms -- yes, he was "special" in that he was an exceptionally good man. We all agree on at least that. What we're saying is he wasn't
supernatural.
I have issues here all around this area. Why did Maggie leave Thomas behind?
WOJ addresses that specifically -- she left him behind because she saw him as a baby shark, able to take care of himself.
If she was hiding from Eb how did he learn how she died?
Ebenezer has contacts; and he apparently met Malcolm. I get the feeling that, toward the end, she wasn't so much "successfully hiding" from Ebenezer as Ebenezer was, "not able to find her, guys, seriously," just like Ramirez
totally couldn't find Molly after Changes.
And why does he know anything about Malcolm if they hadn't been in close contact?
This is an unknown, but not implausible. There are a few possibilities that spring to mind:
1. Ebenezer found out about him after Maggie left Lord Raith. Maybe he was trying to reconnect to her and bring her into his protection. In any case, he sees Malcolm and decides to check out the guy who's dating/married his little girl and, perhaps after getting a Soulgaze going, he decides to leave them be.
2. After Maggie Sr. dies, Ebenezer comes to Malcolm, possibly considering taking Harry himself. Same as above, possible soulgaze, and Ebenezer decides that leaving the baby with Malcolm -- and with no connection to himself -- is safer. This is most consistent with what he later says, in Changes, about why he didn't tell Harry.
3. He scried on them from a distance and used his connections to dig up whatever he could on Malcolm.
Now, that he says a soul "like few I've ever seen" leads me to believe he soulgazed him, so I'd bet on #2. But the overall gist is, "He's a hugely powerful wizard, there's not a lot he can't find out about an unpowered mortal if he wants to know something."
And why didn't he protect Harry if Malcolm found him to tell him? It was his grandson. Justine DuMorne didn't seem to have a problem doing so. I mean, something smells.
Who said Malcolm found Ebenezer? In Changes, Ebenezer said he didn't tell Harry because he didn't want Harry attracting Ebenezer's enemies, so his thinking is probably similar here. I would very much believe that any visit Ebenezer made to Malcolm was initiated, incognito, by Ebenezer.