You've a couple options as follows.

1. Use CSS Overrides to override the colors you're wanting changed
2. Install a Joomla template that is Bootstrap 4
3. Attempt to replace CBs Bootstrap CSS file with your own

For 3 you can use a site like the below to generate the bootstrap.css file. The downside to this is the CSS classes are not prefixed with .cb_template so it'll style outside of CB. So you may want to just selectively pull out the CSS that adjusts the colors the way you're wanting and drop it into CSS Overrides.

bootstrap.build/

I'll be reviewing implementing the ability to generate new CB themes using CB Template Changer plugin next week to ease the process of customizing CB. The recommended approach is to review upgrading to a Bootstrap 4 Joomla template, which will also help prepare you for Joomla 4 release.

The good thing would be to have the ability to change colors to match the joomla template ones.

That's the planned improvement for CB Template Changer. That's too heavy of code to include in CB it self since it'll require including a SCSS compiler library.

Could you implement a root color selection so that the CB bootstrap css file will these root colors ? this way would be easy to customize the colors in a first step.

Bootstrap 4 doesn't use the :root colors at this time. We're using a few in CB it self to make CBs template.css file more compatible with Joomla Bootstrap 4 templates without needing to change template.css.