as bandersen suggested partially, and as you might see in Upgrade section of 6.0.4 or in Release Notes of 6.1.0, the sole purpose of 6.0.4 is to prepare FortiAuthenticator system to upgrade towards 6.1 where is a lot of structural changes.
Upgrading from FortiAuthenticator 4.x/5.x/6.0.x
FortiAuthenticator 6.0.4 build 0059 officially supports upgrade from all versions of FortiAuthenticator 4.x, 5.x, and 6.0.x.
All prior versions must upgrade to FortiAuthenticator 6.0.4 before they are able to upgrade to FortiAuthenticator 6.1.0 and later.
[cit. Release Notes 6.0.4 from your link, "Upgrade instructions" section]