I hope that someone more qualified than I am chimes in but until then I will share what little I can.
I know that you need to maintain continuity in the longitudinal member. I have seen a number of people accomplish this by cutting the center member and "boxing" the opening.
Most that I have seen were installing a roof air but the process is identical.
They cut the appropriate sized hole in the roof, cutting the center longitudinal member in the process. Then cross pieces are placed at the fore & aft ends of the hole and abut the cut center member and but into the right and left longitudinal members. Cross pieces welded are welded in place. Finally "cripples" are sistered next to the right and left longitudinal members helping to transfer load/stress along the center member.
Today I took a closer look at some factory holes drilled into the metal. It seems the metal is thin with wood on the other side. I had looked through your photos Roach but somehow missed that your roof appears to have the same construction. I thought maybe yours had other metal reinforcement since it came with an escape hatch.