Most people don't remotely know how Webpack works. And they shouldn't have to! Same for most other developer tools. You need a few people who can dig out issues if they arise, but most of your people will be concerned with actually building things on top of those tools.
When every team starts a new project from every few months to every few years, having a boilerplate setup quickly becomes very valuable. The added benefit that third-party boilerplate has is that you don't have to maintain the whole lot yourself.
Needless to say these upsides don't come without issues, security and accountability being the big elephants in the room, but popularity helps here, too. The boilerplate is used by a lot of people, in organizations both big and small. If an issue arises, you can usually collectively work out the problem very quickly. It doesn't make the issues go away, but it gives you a good balancing point.
As a tradeoff versus either setting up every project manually or maintaining your own boilerplate project, it's definitely worth consideration — it might not match your needs, but it's a strong option.