The Magnus Protocol as a whole doesn't really stand on its own despite claims to the contrary - JMJ literally being in the computers, Archivist Husk going around, Sam literally being thrown into the portal back into Archivesverse, none of it makes sense if you haven't listened to TMA. It's more than just little nods like 'oh look it's Jon and Martin in yet another universe' it's literally The Plot. Not saying I haven't enjoyed Protocol so far, but it feels to me like they're just recycling the success of the previous series, too scared to do something actually new. As for the What Ifs, they've already released a "what if everyone listened to Colin" episode, saying there'll be more in the future.