The setting for the BlobTempStoragePath and BufferTempStoragePath in our SSIS package is @[User::TempStorage].
Am I correct in assuming that this will be the TEMP location for whatever windows account is running the SSIS package i.e the SSIS Proxy account?
Yes, you are correct unless you are executing the packages with a domain user, domain users do not have the folder 'C:\users\[username]\AppData\Local\Temp\'
http://www.bimonkey.com/2008/04/blobtempstoragepath-and-buffertempstoragepath (Monday, April 7, 2008)
Under normal circumstances, SSIS will write to the default location for these settings – a space in the executing users Documents and Settings folder. In Development, this rarely matters as developers will be executing packages as themselves, and will have rights to their Documents & Settings folders. In production, if you've deployed correctly (i.e. with a domain user executing the tasks) the domain user will not have that folder.
I'm looking at an alternative to having to hard code a location into the BlobTempStoragePath and BufferTempStoragePath settings for each data flow task in all SSIS packages in all our environments which would be a major pain.
I would highly recommend not hard coding these locations. I would suggest using the package configurations setting to populate the variables. That is what we do. We store our configuration settings in a SQL Server database. In that db we have tables for global settings (i.e. configurations for connection managers) and tables for the individual configuration settings for each solution, that way, when your path changes, you only have to change it in one place without opening any packages and redeploying.