run the IDE exe directly (not from within steam). ie, i launch from a shortcut to:
C:\Program Files (x86)\Steam\steamapps\common\App Game Kit 2\Tier 1\Editor\bin\AGK.exe
you'll lose some steam functionality like AutoUpdates if you have that applied & Workshop, and your time spent in AppGameKit won't be applied to you steam "hours on record" if that matters to you.
ack: i might be remembering wrong where i just launched AppGameKit from within steam and with the Steam Integration ticked and still see no steam pop-up :/