You say “Removing seat stays will reduce the amount of weight transfer you are getting from the seat”
The physics do not support this statement. If the rear tire is off the pavement, weight transfer = 100%. 100% = 100%. What is really going on is the LOAD PATH is different. If you add struts, the chassis is loaded differently. With no struts, driver mass is reacting to the frame seat posts. Because of their location, they tend to flex up the rear cross member more.
When you add struts, now more load is going direct to the tire contact patch. The chassis, especially the rear cross member, is not loaded as much. But weight transfer is the same. 100%.
Now, if you change the rear track width, or raise/lower the driver, then weight transfer IS DIFFERENT, so you are correct there. Think of the driver as a lever arm, and the axle as a lever arm resisting the driver forces due to cornering. The ratio of CG height above the contact patch to the rear track width determines weight transfer. Say you were at 1390mm on a gripped up track. You went full wide at 1400mm and the kart was noticeably better. What do you do? You mount the seat lower.