AutoSys uses either the profile specified in the job definition or if one is not specified it defaults to the /etc/auto.profile.
If no profile is specified then the agent will source /etc/auto.profile. If a profile is defined in the job definition then the auto_remote will source that profile. Please note that the profile MUST be in Bourne shell format. Also note that the behavior is changed in the r11 version. For that version the auto.profile is always sourced and if a profile is specified in the job definition it will then source that as well.