Why are time-based deliveries sometimes not awarded an S rating even though delivery time was within the limit?

You need to complete order in less than 20% (or 1/5) of order time limit. So to get S rating for 35 minute limit order you need to complete it in less than 7 minutes.

Cargo damage also affects results:

Scenarios for 25 minutes premium delivery (hard):

• Completed with 5:20 (0% damage) - RATED A
• Completed with 4:30 (9% damage) - RATED A
• Completed with 4:30 (6% damage) - RATED S

Source