You can use BE to perform the backups of VM using the SAN transport mode. Using SAN transport mode for restore was removed due to issues founf with it.
Please refer to the following technote for the same:
http://www.symantec.com/docs/TECH178741 : SAN Transport mode removed from available transport modes for restores using the Agent for VMware Virtual Infrastructure (AVVI)
Note: If you still want to use SAN transport mode for restore then you will have to go back to BE 2010 R2..... but this is not recommended.
Maybe, maybe not...not to be difficult, but there might very well be changes between the versions that could lead to some sort of incompatibility or unstable system.
If you don't have too do so, then don't...
If your query is if you can use Backup Exec Database (BEDB) of BE 2012 back to BE 2010 R3 then firm answer is NO. You can not downgrade BE Database. It will never work.