I don't think that the issue is with "best practices," or any other type of dogma.
I think the main issue, is that companies tend to hire folks that aren't especially skilled at what they do, and rely on excessive structure, to compensate, or that they don't stay around, long enough, to get comfortable with the structure.
This can apply to both newer folks, who don't understand the system well enough to effectively deviate, and ones with a lot of experience, who have allowed themselves to get so hidebound, they are afraid to deviate.
As I have gotten older, wiser, and more battle-scarred (often, from self-inflicted injuries), I have learned that "It Depends™" is the only true mantra for my work.
Usually, best practices/dogma/structure becomes important, when the codebase is being worked on by a team, and when there's the need to coordinate work between teams.
There's some type of work that just can't be done, without structure. I've done that type of work. Other work can be killed by too much structure. I've done that kind of work, as well.