Yes, that part I get fully, but the OP wasnt asking which would be stiffer between the two bike, simply pointed out that he now has a different bike, with the option of two springs for One bike, so the the two springs<given two would actually be the same.... but lets not get into the inaccuracies of steel springs> Two stroke length spring, one shock, one bike, same rate.....Same feel for that particular bike.Even though they are identical spring rates the 350/2.8 on an 8" travel bike would feel ever so slightly stiffer than a 350/3.25 on a 9" travel bike due to the difference in leverage ratio (assuming identical leverage curves.)
What you need to do is calculate the wheel rate:
Wheel rate = (ratio)squared x spring rate
1/3 squared x 350 = 38.88 lb/in
1/2.9 squared x 350 = 41.61 lb/in
But yes- on the same model year bike with the same leverage curve they will feel the same for a given amount of travel. Changing the length of the spring will not change the wheel rate.