You still get the loot you had already earned. It will show up the next time you finish anything and get an expedition complete screen. Just pop into freeplay for a moment, then exit.
I don’t use controllers, so I can’t compare. I will say that the Flight/ Combat controls are pretty fantastic now with M&KB. My colossus flies like a crazy combo of an A-10 Warthog and a Sopwith Camel (it took some tweaking and experiments with the settings).
Lastly, here’s a map for a bunch of the overworld chests. Keep in mind, it’s still random – they have a chance to spawn, but not a guarantee.