After discovering the "Processing" option "Use replaygain" isn't used to scan the files automatically after encoding I figured this would be a good option to include.

So if any files are being encoded the replaygain scanner could be activated right after the encoding process.
The only problem that might occur is when to use the album scan and when to use the single file scan. Scanning multiple files doesn't always mean they are from one and the same album.
To get around this problem you have to alter the encoding settings each time you're going to scan (assuming the worst case scenario of mixed encoding and therefor not always encoding complete albums), or the question of using album or track scanning could be asked each time you're starting to encode with the replaygain option enabled.

An automatic detection could be used as well if multiple files have the same album name but this might not be preferred in all cases of encoding.

Having that said it might be too much fuss including this option in the first place but maybe someone else has a better solution.