As the article goes into detail, a big factor of costs ballooning is that the municipalities explicitly ask for much more stuff than initially planned - as you

As the article goes into detail, a big factor of costs ballooning is that the municipalities explicitly ask for much more stuff than initially planned - as you say "unless its for something outside of what we specified together and they quoted", which is the exact thing happening in the examples provided by the article. You ask for A, get quoted $X; but if then after the public input (which, as the article states, can't be avoided or its suggestions refused, because votes and politics) you decide that you actually want A+B+C+D+E+F+G (it's not an exaggeration, it's common for the "add-ons" to require multiple times more work than the initially requested thing) then you're not getting that for $X no matter how you write the contract. If someone is painting your house and halfway through the process you discuss with your family that it needs to be a different color (redoing the already painted parts) and the kids room also needs to be painted, and oh, they should fix the porch before painting it, that's going to result in cost ballooning far above the quote.