With the Absolute Music problem, what album were the songs part of originally because when i look at the report it seemed they were already part of Absolute Music. Could they possibly have been in no album folder at all, in which case SongKong would just do the best it can with what it has. Perhaps you could run Undo changes on these folders.
Going forward you can force SongKong to treat all existing folders as album folders without exception by enabling Match:All existing folders represent a single album
Hard to say what has happened with the Pink Floyd album, were the mp3 and flac versions originally i same folder or a different folder. Maybe Format:Add Audio Format to Release Title would be useful to you.
Also if you are happy with the folder organization of your files before modifying with SongKong you can enable renaming files from metadata but without changing the folder part by enabling File Naming:Rename filename part only[i]