Welcome to our world, Lynchgate.
Some time back, I started this other thread on exactly that problem
, only to get distracted by life's many heavy responsibilities such that I did not expound on the problem.
I never did post pics of what I found, which thankfully was nowhere near as extensive as what YOU found. We had incipient corrosion of the same type. We had one tiny perforation that was starting to allow rainwater in, plus a patch of rust around each of the rear rack feet.
I sanded it, phosphated the hell out of it, then POR-15'd the hell out of it, then Rustoleum'd over the POR-15, then re-caulked it within an inch of its bloody life.
But those were intended to be stopgap measures only. Just to hold us over until we find the time to do the REAL work (we are big DIYers
The entire roof rack needs to come off and get replaced. But we have a solar array up there, so that's a big job. My husband is a Mech E and he has a design in mind to replace it, but that's for the future.
I digress. Your damage is obviously too extensive to be patched with similar bubblegum, even temporarily.
The only other person of whom I'm aware who had to do a similar roof patch is Maggie (Lily&me), because of analogous corrosion around an antenna. She contracted the work out, and if she could chime in here, maybe she would have some suggestions for you.
But wait - there's more.
There's also the issue of how much damage you might have behind your finishes because of the extent of that mess.
Of particular concern is the plywood subfloor. If a lot of water worked its way all the way down into it, you might have an undiscovered mess. Another user on here a couple of years back discovered that his subfloor had essentially been reduced to the consistency of coffee grounds because of rot. I never did learn what became of him / them - AFAIK, he stopped communicating on this forum. But he had very little structural integrity left in the floor and that's a big, big problem.
So, you might want to check the van widely before you undertake any work, in order to first confirm that it's not already a write-off that is not worthy of at least the paid investment that it would take to render it whole (extensive DIY would come with a different calculus).
I hate to put it in such stark terms, but there's just a lot that can flow from that degree of roof damage. Crap rolls downhill. So does water.
Keep us posted, please.
EDIT: Here's the previous thread about extensive damage to the floor of the other owner's 2005.