iTunes Doesn't Won't Let Me Use An Alias Folder To Save iOS Backups in macOS Sierra?
A slight correction in terminology may help. Theres no such thing as an alias folder at the Unix level, but what you are actually creating is a soft-link to a folder.

Depending on how the target is specified ln may not complain if the folder still exists, but it will not overwrite it. I find it's safer if I am in the folder I wish to create the soft-link in.

I have setup the following on Sierra and High Sierra, and it works correctly:

$ cd ~/Library/Application\ Support/MobileSync/
$ rm -rf Backup
$ mkdir -p /Volumes/EXTERNAL_DISK/iPhoneBackup/Backup
$ ln -s /Volumes/EXTERNAL_DISK/iPhoneBackup/Backup Backup
$ ls -l
total 0
lrwxr-xr-x  1 user   staff  35 10 Oct 21:16 Backup -&gt; /Volumes/EXTERNAL_DISK/iPhoneBackup/Backup


Now start iTunes and try the backup.