G'day Alex, don't cut the stern frame, I think it is just an optical illusion, I have posted some pics below that show mine during construction, I had the same fears as you I thought mine was too high as well, I will try and explain with the help of the pics,
First of all the little tab at the top of the frame between the two letters X needs to be removed before attaching the deck as the
rudder comes up against the back of this frame and if it is not removed now it is a hell of a job to cut it off later,
I don't think there is any difference between your frame and mine it just looks it, First there are two beams in the kit that go
across between the X,s, that lift the height in this position,
and after the beams are in position the deck should sit in
line with the black dots,
a pic of mine showing the beams above the X,s
overall view,
this one shows the ply deck glued in place,
I hope this is clear enough,
best regards John,
.