It appears to be a common trend though, I guess because most content is now on apps and those websites only advertise apps or services.
The layout is really up to you.
https://github.com/HackerThemes/theme-machine/blob/master/th...
https://github.com/HackerThemes/theme-machine/blob/master/sc...
which is imported in the file that you linked. That's all in terms of SCSS. Then the gulp task runs the SCSS build and the autoprefixer.
It's surprising always how little you need to tweak Bootstrap to make it look completely different.
I dont use bootstrap themes like this myself directly but they can have a very useful purpose (which I intend to take advantage of)
Suppose you release an application, it doesn't matter if it's OSS, Commercial, or even hosted SaaS. It's a business web-app, so you use Bootstrap as your "UI Kit". Ok, Bootstrap has some basic default styles, and you maybe have a designer create a custom theme for your app.
But the user/customer wants to customise the appearance, perhaps it's exposed to their clients somehow, perhaps it's visible on a physical terminal in a shop.
Either way - this is where bootstrap themes (and I mean themes, like these - not so much those "Bootstrap Dashboard" which use a whole whack of extra JS libraries, markup and css) like the linked ones, or those found on https://bootswatch.com can be very effective.
If you build several applications, the effect is magnified, as the customer/user can now use multiple apps with the same custom theme, with almost no work at all from you.