It only deduplicates *within* a backup archive. If you backup the same file to more than one destination you'll have the file in both destinations independent of one another. Each backup destination is a complete independent backup which is the point. If one backup destination depended on another having two would be somewhat useless.

Deduplication mainly is useful for slow bandwidth connections. If you have multiple copies of one file in different folders, it only sends it once. It works locally and only keeps the one copy though. If one of the files changes then it stores new copy in the backup and the old one stays for both locations as it's part of the history. If only part of a big file changes, it only sends the changed bit.

The big number is the GUID of the machine. Every install or machine has a unique number to identify it. So yes the base filename on each of your destinations will be the same.

Stop trying to understand the files, do you backups and do spot checks using the Restore tab to see what you have. Disconnect backup destinations to simulate lost drives.

You lost me with M:\ and E:\ but in theory they should be the same size if they are the same source data. Note that as soon as one destination misses a backup e.g. you unplug for offsite, the size will change of course as one will grow without the other. If you plug it back in it should catch up but will have missed any intermediate changes of course.