in the plugin’s 3.48 version you’ll find the “Where in site: In Block editor” option on each “Add/Edit Custom Code” page. If the option is enabled, then the custom CSS/JS code will be applied on any page/post editing page with the Block editor, as well as in the FSE.
Could you give me more details? What is exactly the custom CSS/JS code that you want to add to FSE (copy/paste the code, preferably in https://pastebin.com/ and link it here)? What theme are you using? Is the custom CSS/JS code not showing up on any page, or does it happen only for specific Pages/Templates/Patterns/Navigation?
For example fonts that I am using which are showing on the front end do not show in the back end. I have used the inspector to check if the css is being applied anywhere in the backend but it does not appear to be. I am using the Greyd theme. I can give you access to the website if that would help?
Would you copy/paste the custom code that should load the fonts, preferably in pastebin.com and link it here?
You can provide me a link to your website, though that will hardly help. But getting admin access to the website is definitely not allowed by the WordPress support forum rules, nor am I willing to accept the responsibility associated with it.
Unrelated to the plugin’s ability to apply the CSS/JS custom codes in FSE: the block themes have a built-in method for uploading or installing fonts directly from the FSE. This is a feature added in WP 6.5. See this article for more details.
Nevertheless, I still want to know the use case in which a custom CSS/JS code added with the Simple Custom CSS & JS plugin doesn’t show up in FSE. With the information at hand I’m not able to replicate the issue, so any additional information would be helpful.