Pop top roof rot

It is hard to really comment without being able to see exactly what you are talking about.
What is the structure underneath made from? Wood/aluminum extrusion?

For the $3500, were the caravan repairers repairing back to new condition? Depending on what standard you are willing to accept you can just bodgy things up, but a repairer is unlikely to want to do this as you would still want some sort of warranty and they won't want to cover a 1/2 arsed job.

I'm not a fan of silicone sealant, it often doesn't stick well and it it comes away, getting anything else to stick to it is difficult. Polyurethane sealant is a much better option, is more UV resistant and more flexible.

Sticky tape, wasting your time really.

If you could post some photos of the van and some close ups of the damaged area then it will help others to identify possible fixes.
The professional repairer (as has been pointed out)will be looking at a permanent repair whereas a Fudge may do to keep the cost down. As it is a hold down catch area it needs to be strong enough to do the hold down job as well as keep the water out.
Regards
A

Lindie.
As a temporary fix if the surface on exterior is "reasonably" clean , you can purchase a tape named "Gorilla Tape".
It is an extremely strong product and good in exterior applications, with a very good resistance to the elements.
I have a flexible solar panel on the fibreglass roof of my RTT and it does an excellent job holding it down, and yes there is silicone on the underside but tape acts as an excellent flashing so to speak, and highly resistant to shrinkage.
Unfortunately I think it is only available in black and not paintable.
Alternative method could be to speak with someone experienced with fibreglass, and with a little flywire on inside they may be able to "glass" both sides of the hole.
Cheers & Regards
Flighty

"total roof rot on the inside"

Lindie, I think you have just discovered the major (and expensive) problem with all older caravans - dry rot - which is caused by water infiltration into the wood of the caravan frame.

There are very few vans that don't leak water into the frame after about 10 yrs.
This is because a vast number of caravan designers/builders have no interest in making their 'vans last - and they very often don't have any idea of what constitutes good design that thwarts water entry into the frame.

It's not helped by the fact that cheap and lightweight Asian-source timbers often comprise the majority of caravan frames - and these timbers have little ability to resist rot, once wet.

Repairing the frame of caravans that have rot problems is time-consuming and expensive - and rarely is there any short-cut.

The outer lining and trim has to be removed to allow access to the frame, and then the rotten portions removed and replaced with new timber.

This is the only way to ensure that the frame has integrity, and that you can secure other exterior parts to the frame with confidence.

One caravan repairer has a website full of photos of caravans damaged by rot, and it's a pretty depressive site when you see the endless amount of work this bloke has, repairing them.

I don't think any kind of adhesive tape is going to cure your basic problem. If the roof frame has rot, it has lost its strength and integrity, and travelling at highway speed will eventually make the roof come apart.

(speaking as someone who has just had a caravan door part company with the caravan, because the wooden door frame had unseen/unknown rot, and the door frame just broke apart at highway speed).

Cheers, Ron.