Disney QA/QC standards and documentation, PDR/DR and related meetings and submitted documents certainly increase costs and were on level with or exceeded the federal / mil-std work I have seen.
Toss in challenges related to foundation and change orders during design... It doesn't really surprise me too much.
I can point to two Disneyland Paris roller coasters as to why they overengineer their rides now. First, Indiana Jones et le Temple du Peril is an Intamin looping coaster that was pegged as "temporary" and was soon plagued with structural issues. In 1999/2000, when they added the 12 passenger trains, they had to change quite a few track sections. Next, in 2014, the ride was closed and the temple made "permanent" with new materials and the track itself had a major change: the loop was unbolted and a specialised construction company from Germany came in to yank the loop out. They used a tall crane and they were able to move the loop vertically, not damaging the rest of the attraction. Vekoma in the meantime engineered and fabricated a new loop that fit in the same space, yet was able to take "Disney loads" and have a smoother shape. The same company came back, assembled the loop on the ground and then reinstalled the loop. Impressively, this whole refurb only took 5 months!
The second attraction that had major issues was Space Mountain: De la Terre a la Lune. The ride was originally delivered with 6 trains, five of which could run at the same time. Alas, the tight layout, high forces and extreme cycles meant that by 2000, a short 5 years after the ride opened, the train chassis had to be replaced. The original chassis sourced by Disney were unable to take the loads and Vekoma designed and fabricated new weldless chassis. The idea here was that by minimizing welds as much as possible and by using bolts and large cast steel pieces, they would have more durable chassis. It worked with one slight issue: the new chassis were heavier than the old ones and it caused timing issues on the ride. Basically, when running 3 trains on one station or 5 trains on two stations then, the new trains would catch up to the old ones and cause ride breakdowns. As the old car shells were recycled and just bolted on top of the new chassis, the solution to keep the last row empty? Grab large Mickey and Minnie plushes and strap them in the back row. The cast members would keep the back row empty and when they spotted the two VIP guests, they would not send guests to fill it. Once all the trains were switched, Mickey and Minnie finally ended their endless rides.
In addition to the heavier cars, running five trains also put a ton of stress on the structure and when they did Mission 2 in 2005, the ride launch was reconfigured and removed the ability to run five trains. The most you can hope for now is two trains on one station or four trains on two stations. After that, Disney moved to the current specs that exceed anything you can imagine of and the rides are now able to take the cycles without complaining.
One perfect example of the overengineering is Expedition Everest. Did you know it was originally designed to run four trains at once? Since it has the best cast members on property and after carefully examining the design and testing, Disney was able to buy an extra train. It can now run five trains at once, giving it even more capacity and I have to say this: GREAT JOB DISNEY!