Document feeders are a fixed size so it makes sense that Use Custom Size is not available when that is set.
As for the software not prompting you for multiple pages, when you have the detect separate images selected then I would not expect the software to prompt you to load the next page. If you wanted to scan additional images then you would just load the next sheet of paper on the flatbed. With the file name set the same then the following scan would have Image 3, Image 4, etc.
If you wanted to scan entire pages and save them as one file then if you select PDF for the file format you get a setting "Combine into single document". Note that you don't get a prompt to load the next page, but if you press the scan with the next page loaded, the scan is added to the first page. Note also I only have a flatbed. With a document feeder the process may be different to what I describe.