due to Elementor 2.5, GP Sites using that pagebuilder no longer auto updates the Sites URLs after import. This should not effect any sites that were installed previously though.
During the installation the site library installer prompts you to update your permalinks. Let me know.
GP doesn’t add the lightbox, its probably the Elementor one.
Edit a page in Elementor, Hamburger Menu > Global Settings > Lightbox. Here you can disable it.
The missing image on the home page is being requested from the shortpixel CDN. So i am not sure why its not displaying but i would start by looking at that plugin to see if theres a problem.
I am not sure what to advise the issue could be with ShortPixel or Elementor. One common issue that does arise is Security plugins or server firewalls could be blocking shortpixel