I think you are misunderstanding the purpose(s) of the alignments file.
It serves as:
- convert - The document which tells the convert process where faces exist in the source for swapping
- general - Holds information about all the faces it has found within a particular source
In regards to training, the alignments file is not used (directly) at all. The information that is held in the PNG header of each training image is the same as the information that is held in the alignments file.
So why keep the alignments file for training? You don't have to. You can delete it. However it is the master document that contains information about the faces within a particular source. By keeping this alignments file, you can quickly and easily re-extract the faceset from the source file by just keeping the source and the corresponding alignments file. There is no need to keep facesets around, which take more space on the disk, and also the information in the PNG header may go out of date as the process moves on.
However, there is nothing stopping you deleting the original source + alignments file and just keeping the facesets. However, without the alignments file + source you would be unable to perform any edits on these faces going forward (technically, you can re-generate alignments files from a folder of faces, but that's out of scope here).
Ultimately, it's a workflow thing. For me, personally, having 10 source videos for an individual + 10 cleaned, fixed and corresponding alignments file means that I can quickly regenerate face sets for this individual..