It could be down to particular project managers just being bad at haggling. If you tell someone 'we have £x, and we want to do this', but it doesn't cost £x, that person won't complain. So they'll just say yes, and an inexperienced / gullible / simple project manager which just hand the money over and get on with it. A better PM would try and reduce the price, get more or go in with a lower initial price. And given that Th13teen was very tight with opening (I believe the queue line was finished the day it opened?), that could also make sense.
For another example, Zufari had a major budget cut - I think they slashed the budget by 40%, but the ride ended up largely as planned. So they probably realised that was the case, and instead of doing more stuff or paying more for the same product, they just saved their money.