Emails from addresses listed in the system safe list being quarantined due to dictionary

That Cookbook would not be a solution.

BYPASS (now called SAFE) does not bypass Content Profiles:

"SAFE: Relay or proxy and deliver the email, only if the recipient belongs to a protected domain or the sender is authenticated. All antispam profile processing will be skipped; but antivirus, content, greylisting and other scans will still occur."

http://help.fortinet.com/fmail/5-3-6/admin/index.html#page/FortiMail_Online_Help/policy_09_10.html

Use additional Recipient Policies where the sender is specified as what needs to bypass the Dictionary Profile(s).

Move above the existing policy and apply Content Profile without the Dictionary Profile.

Or if suitable, set the Dictionary Profile on an AntiSpam Profile rather than Content Profile so that whitelisting bypasses it.

"Is there a description or chart somewhere that describes and details the flow chart for all the filters and lists that an incoming email is subject to?"

Refer to the order of execution: http://help.fortinet.com/fmail/5-3-6/admin/index.html#page/FortiMail_Online_Help/overview_01_24.html