You should be able to use glTF (RHS) assets out-of-the-box in a a LHS Babylon scene, but it sounds like this isn’t working correctly in your case, which we’d love the chance to fix. Could you share a repro of the issue in a PG so we can diagnose? 
Also, just to confirm here:
a past update flipped the Z axis when we were RHS and broke our input system
Are you referring to this breaking change?