Yes, Divi Booster is compatible with the Divi Builder Plugin.
There are a couple of things to note, however.
Not all Divi Booster features apply to the Divi Builder Plugin.
The Divi Builder plugin makes a subset of the Divi Theme's features available on other sites – specifically the Divi drag-and-drop page builder and its modules. Other things such as the Divi header and footer are not made available on other themes (which typically have there own). This means that Divi Booster features for things such as the header and footer won't work on other themes, while the Divi Booster features targeting the Divi Builder and its modules will.
In practical terms, this means the settings in Divi Booster under "Divi Builder" and "Modules" will work. A few others will too, such as the "Developer Tools", and yet others may partially work, such as the "CSS Manager". The remainder won't work on other themes.
Divi Booster Settings Page Location
When used with the Divi Theme, the Divi Booster settings page can be found by going to "Divi > Divi Booster" from the main WordPress menu. When used with the Divi Builder plugin, however, you currently need to go to the plugins page and click the "Settings" link next to Divi Booster.
I'll be looking to further improve the Divi Builder plugin support and integration in future releases of Divi Booster. If you spot any problems, please let me know.