we installed the Emek arch which I believe is heavier than the Atlantic arch. I have a similar distribution of heavy items, 80m of 10mm chain, two anchors forward, dinghy on foredeck and a 9.9 hp outboard in the lazarette. I haven't noticed significant change in the waterline aft, in calm water the red stripe is dry. The front does look like yours with the red strip higher above above the water. I seem to recall that it looked the same before the arch was installed.
We do get the slime/algae build up at the stern where the water continually slaps at the hull. I don't know if moving the boot strip and antifouling line up will help much with that.
Is your engine exhaust port under water? Mine sits right at the waterline, in fact I changed the exhaust hose while in the water at a marina. Water was about 1 inch below the port.
SV Annie, SM 37
Druif Bay, Water Island USVI