Did you read the note below the paragraph you quoted. Seems pretty explanatory. If you ordered the ticket through PFC or Global travel they cover 100% of the change fees if the company changes the pairing.

Note: When a deviating pilot arranges for the booking of his deviation travel, either via an electronic system(s) or by phone contact with the Company’s travel department or vendor, the Company is responsible for any of the above-listed fees that may be incurred due to the cancellation of the scheduled travel, and/or the booking of the pilot’s deviation travel itinerary. However, in the event the pilot makes any subsequent changes to his deviation travel itinerary, and if those changes result in any of the above-listed fees, he shall be responsible for those fees.