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Many large organizations will insist on 'service accounts' from their Active Directory to run processes like FMS. Helps set explicit security, helps with security audits,...
Other reason is that you may want to use the FMS scheduler (especially the script sequence or OS script functionality of that) to touch resources outside of the machine itself (network shares, other services,...). In order to secure that you'd want to set up an explicit account with just enough rights to do that, and run FMS as that account.
On windows, the default account is 'local system', which by definition has no rights whatsoever to anything except the machine it is on.