I figured out the issue and leaving this reply just in case anyone else stumbles across it in the future. Totally unrelated to symfonium and exclusively to beets.
The root cause for the issue is the “Edit“ plugin I use sometimes to edit metadata after import. To be specific, when using the -all flag (load all metadata) to edit metadata, the R128_ are shown as editable fields, default “0“, and, will be written to the files as empy tags, if you dont actually edit them.