if your in manual and flip to atti, it goes down with the extra weight more than if it's lighter? Are you sure the throttle doesn't have any trim and that you put it at exactly 50% when you calibrated it?
everything your seeing is exactly opposite 2 of them here that are over propped with 9's 1000kv and on 4s, they weigh 2100 and 2300grams. They hover in manual at 1/3 thorottle and atti it hovers at mid stick. if i hover in manual and just hit the switch, the throttle is in an ascend spot, 1/3 stick. if i add the second packs, manual hover is exactly at 1/2 stick and when it's flipped to atti, mid stick is already being touched, hovers
If you wanted to get to radio programing, you could make throttle curves for each mode like manual mode move the midstick to 30% and leave the mid stick at 50% for the atti and atti gps mode.
Some radios might need to be in heli mode to see throttle curves.