You can use Bootstrap from the source SCSS, and cherry pick the features you’re using.

@import "~bootstrap/scss/_functions";
@import "~bootstrap/scss/_variables";
@import "~bootstrap/scss/_mixins";
@import "~bootstrap/scss/_root";
@import "~bootstrap/scss/_reboot";
...

You can even inject your own overrides for the bootstrap variables before hand, before other mixins/components that use them. It’s how I prefer to use Bootstrap in projects.