Please do next tests:
1/ Try to disable all the third-party plugins (including cache plugins), that does not come bundled with XStore https://xstore.helpscoutdocs.com/article/36-included-plugins , clear the cache of the browser, and check then. Maybe one of the additional plugins is the reason for the problem.
2/ When the Email builder is disabled the problem with 2 emails persists?
When we register – only 1 mail is received – https://prnt.sc/PuzUzKZE3cCq (not from the Builder), so it seems you better understand the situation, so please do mentioned tests and let us know.
One standard license is valid only for 1 project. Running multiple projects on a single license is a copyright violation.