You know...
Why would ATs and Spirits disconfirm characters anyway?
Okay, hear me out. Look, in order to force it so that ATs and Spirits don't overlap with 1st Party (and some 3rd Party) DLC characters, those characters would have to not show up in any form whatsoever within the game (at least in the parts a normal player can see).
Let's say they were making (pulling a character we know is a spirit) Dixie Kong as a DLC fighter, when people get the game, fans will realise very quickly that Dixie is strangely missing from all parts of the game. This would immediately give away that they are doing something with Dixie (because she recently appeared in Tropical Freeze, so there's no way anyone would be justified in saying she's not important enough to show up or some claptrap like that).
This goes similarly with my thoughts on Isaac; let's say they're making Isaac as a DLC character, they would be justified in not including him as an Assist Trophy because he'll show up later, but that creates a minor problem; because of the general secrecy surrounding character inclusions, fans of Isaac will be left wondering where Isaac was had he not shown up as an AT, not only that, but there are Golden Sun spirits in the game (Felix and Matthew have been discovered), so if Felix and Matthew were spirits and Isaac was a no-show? That'd elicit a big "HMMMMMMMMMMM!" from the fans.
If Golden Sun didn't appear at all, then that'd send the wrong message to the fans (that Golden Sun isn't important enough to get into Smash).
What's better? Causing minor disappointment by introducing Isaac as an Assist Trophy before (hypothetically) DLC, or causing major disappointment (and/or rampant conspiracies) by not having him at all until (again, hypothetically) DLC? Not only that, but Isaac's appearance spurred Golden Sun fans to rally together to show their love for the franchise, which might not have happened if Isaac wasn't an Assist Trophy (because of crushed spirits).
I don't know, maybe I'm rambling.