Installation fails with missing "file" -plugin error
Yeah, got this sorted. 

The reason for this strange behavior was unsurprisingly misconfigured field in some entity's baseFieldDefinition method.

Someone had used in display plugin configuration "file" instead of correct "file_generic" and for some reason this hadn't been triggered before this. The app has been live for about 6 months and gone through numerous updb's and entity-updates.

This was a nice one. I'll just leave this here in case someone has same mistakes :)