Pop-up and pop-in windows are a good way to display low-volume content over the main window. However, if the contents of these windows contain strategic expressions on which you want to rank, these pages may not be accessible by any search engine. Alternatively, they can be seen as a page with a dedicated URL / separate from the one initially consulted.
Never host any strategic or high-value content in a pop-up or pop-in window. If the content can enhance a page and strengthen your SEO, use it directly in the html source code, without using this overlay.
Example of pop-in impacting SEO:
The content would have more impact and would generate more interest if it appeared on the page.
Example of pop-in not impacting the SEO:
The window has no strategic elements that could potentially help the page rank better on Google