Tried with different liveries from flightsim.to, they no longer appear as a variant for the A340-600. Do these liveries need to be updated or something changed related to liveries location?

Yep have the same problem. No liveries work from .to, and it takes ages to see the included liveries to show up in the menu

Also seated passengers desapeared from GSX option list

Same problem with 1.0.4

This is likely because the aircraft changed to a native model in version 1.0.3 and higher. As such, third party liveries will need to be updated appropriately.