Hmmm… I’m not sure what to offer on the #2 panel sitting lower. I’d recommend contacting the guys at CLC and getting their opinion.
As for between the side and the hatch, I accidentally ended up with a larger ‘gap’ than I had hoped for on one side. For me, I identified it as being due to an ‘alignment’ mistake when I was mounting the hinges. My goof, but I plan to fix it at a later point in time after I’ve got some miles on it and have determined if it really bothers me that much. What your picture shows doesn’t look any worse than what I ended up with on that one side.
In either case, I’d recommend talking with CLC. Their customer support is fantastic, IMO. I’m sure they’ll be able to get you the right solution.