I believe you are correct, your rifle case will count as one of your two.

we did exactly what you are asking, we packed alot of gear in our cases.
I had my skb bow case, put hunting/fishing gear in with the bow.

my partner had an alum sided rifle case. all of our fishing rods and gear went in with the rifle.

1 carry on ( just like you did, my hunting backpack, with bino's gps and range finder.) rain grear and one change of cloths * just incase my suite case didn't show up.

1 large duffle bag with cloths and such.

pack once...wait a day unpack and leave 25% of what you packed the first day out.
do this till your down to what you are sure you HAVE to have. all the rest is dead weight.