It’s important to understand that just launching Maya regularly from your system’s OS will not launch with AYON. You’re required to launch the applications through AYON’s desktop launcher
Even though this guide was once intended for OpenPype the concept remains the same; you’ll need to make sure you are launching Maya like that in a task. It also describes the “I don’t see AYON/OpenPype within the application” situation.
I believe your 
Issue has been solved in the Ynput discord community in the Have you launched Maya from AYON discord thread here. 
- linking it here for those reading this forum topic and might need those extra screenshots that got shared there. To recap that discussion:
- You didn’t have any Folder + Task created which were required to launch an application using the Launcher. Once you had that created it became trivial to launch Maya with the pipeline functional.
Generally the tools needed will differ quite a bit. Looking at the current community I assume it might not get a huge part of development focus - nonetheless I don’t see why it wont be possible to integrate AYON nicely within a game studio. (Especially with there already being an Unreal integration, etc.) I believe the biggest culprit is that studios tend to use Perforce or alike which might require a slightly different methodology - nonetheless, I have even seen focus on that within AYON/OpenPype’s development but it’s just not high up my own radar.
Looking forward to it - and thanks for wording your issues clearly! 