The RAAus rules we have to operate under are not perfect but they are what we are stuck with.
I understand your frustration, as I said earlier, get any correspondence in writing, maybe you can try to get RAAus to give you permission to do the repair, you may even manage to convince them it is a minor repair. If you can't I would strongly advise against proceeding unless you have a L2/L4 who will sign off on your work. You may end up with a plane you can't legally fly.
I would be requesting the repair document from RAAus, or get your L2 to request it. They should supply it to him/her.
Also as much as you won't use the plane for training/hire, do you plan on taking passengers? It opens another liability issue if you have done repairs without authorisation.
I fully understand the limitations imposed by the tech manual. It is why I won't buy a factory built/certified aircraft. I went through similar to you when I was looking at the Skyfox I was considering buying. RAAus were aware of the aircraft and made it clear that as a L1 I could not conduct the repairs myself.
That's why my RAAus aircraft are home built and my other aircraft is VH experimental and will not be getting transferred to Group G.
If you can get the repairs done for $1k I would be jumping on it before whoever quoted you realises just how big a job it is. The maintainers I spoke to where talking 4 - 5 times that. Everyone I spoke to said it is a shit of a job and requires a lot more effort than you would expect. Apparently it can't be done without cutting the wing covering.