Even I am seeing the similar behaviour but in a different context. Instead of having multiple windows. I have multiple tabs opened in a single window, and i get the error mentioned by you (
[blocked] The page at about:blank was not allowed to display insecure content from safari-extension://extension.path/index.html?host=https://www.somesite.com&iframeId=id )
when setting iframe src in first tab alone after restroring tabs from last session. But, I am able to set the same from second tab onwards.
Please let me know if you find any solution/can i know if you had filed a bug if it actually a bug from safari
This should be fixed in Safari in the macOS Catalina beta, Safari 13 and the latest version of Safari Technology Preview.
Are you still able to reproduce the issue using any of those version of Safari?