Permits and paperwork are probably mostly a time and restrictions on what and where you can build cost rather than a direct monetary cost. But certainly indirectly have a lot of influence on where and how you can build.
the waiting can be very expensive for individuals as they have to live somewhere. for developers it's more about the indirect cost of having a lot of capital tied up during that time.
then there's environmental assessments, some places have to deal with archaeological assessments too. developers need to pay people to deal with the permitting processes. lawyers are often involved throughout as well.
architects and engineers need to be involved, often repeatedly, if you're modifying an off-the-shelf design too.
as with buying a house, there are a lot of expenses that very few people consider, and are hard to predict even if they do.
Opportunity costs can also be a negative number.