It's likely one of those situations where both the source of the problem and how to deal with it effectively are not clearly obvious to the person who made it. Sounds like he's not seen this before and so he's probably shooting fairly blindly as to how to soundly address it. I used to work in a cabinet shop and I can tell you firsthand that in that place, the carpentry experts were
not the finishing experts and vice versa.
Odie's oil is nice but not a hard, resilient, durable finish, so it may be used by people who are looking more for ease of use and clean results than to create a lifetime finish.

This is a dining room table, it's going to see lots of contact in its lifetime. Either a hard, glassy, gloss surface or a satiny, oily finish will work, but the glossy one will probably protect against these kinds of situations better over time. The oil finish will probably better hide little imperfections that the table gathers over time.
In the end, I think there will probably be some trial and error to both figure out what happened and figure out how to resolve it. I suspect the builder may also learn from this and explore other finishes, or be more cautious around packing and shipping in the future. The "liner" of the crate in the pics looks to be the thing that became moldy and it looks like it was some kind of cellulose based product, which are notorious for getting moldy in damp or humid settings. Overall, it sucks, but I guess what I'm saying is that a very simplistic solution and answer may not be forthcoming, so if it is a meaningful table for you and you love it other than the mold, it should be worth the time, energy and bucks to restore it.
I'd also just put out there from both building these things along with other furniture myself, and seeing prices in my local marketplace, that if you paid less than $5000 US for this, you did great. If you paid more than $5000, then I completely agree the builder should deal with it 100% with little to no involvement from yourself.
Edit: two of the more local suppliers of live edge tables here offer 5 year full replacement warranties on construction and finish problems.