SQL Server: What is the difference when backing up via .bak, BACPAC or just copying .mdf files?
the .bak file is far larger than the actual database. 


The problem might be that you are just appending the backups to one single file. The default is to appended to the device. Take your backups with WITH COMPRESSION, INIT - compress your backup and all backup sets should be overwritten.

A .bacpac file is not a substitute for a full backup.. Also, using MDF/LDF files as backup is not a good habit.