Yes, it does. You can also use Squirrly SEO in compatibility mode. (more information about this available here)
Once you do this, the SaaS part of Squirrly SEO will help you with your SEO, and the code-changing features will be left to your themes and plugins.
You can do Multiple Keyword Optimization using the Live Assistant together with Briefcase in the Thrive Architect Editor.
All you have to do is make sure the Activate Live Assistant in Frontend option from Squirrly is turned ON. You can access this option from Squirrly > Live Assistant > Settings.