we lowered ours about 12" and use it for storage since we don't sleep there... I just found the right height, made two marks thru the holes to know where to drill, and put two similar size holes thru the rail bracket.
the bunk or schwintec system doesn't care where it's located - the pins should hold it in the new position just the same...
never had any problems with lifting it or lowering it in 50,000+ miles since then...
the DW loves the additional storage
'14 Palazzo 33.3 bunkhouse 34' diesel
KingTailgater2 Dish HD, 100w/5a SOLAR, BlueOx
100,000+mi since '14 - US, Alaska, Canada - Hiawassee, GA! (also, '14 Gulfstream Amerilite and '07 ForestRiver Rockwood) : )