You should consider the alternative crossing from Dunkirk to Dover in the 'peak' season. In Dunkirk, there are better organized (simply less traffic, easier to plan ahead) passport controls, and the queues are much shorter.
You can pre-book a Flex ticket which is 50% more expensive. Which is in my eyes way to much and also doesn't answer the core of your question:
Flexibility to amend your booking on arrival at port to travel up to 72 hours either side of your booked crossing time for free, subject to availability.
£10pp (€12,50 p.p) supplement will be charged for each extra passenger when more than 4 in a vehicle. Charge does not apply to infants between 0-3 years old.
No administration fees – only pay the difference in the fare to travel more than 72 hours on either side of your booked crossing.
Full refund up to 48 hours before travel.
Buying your tickets at the ferry terminals in Calais or Dunkirk (a few minutes away) is just 'another lane' you have to go to and wait for. It would take about 30 minutes to a few hours extra. (peak-season) And the price will be €5 (DFDS) to €6 (P&O Ferries) more.
When booking by phone or in person, you must pay a service fee of; £5 / 5€ on the Dover-Dunkirk and Calais routes.
Another option is to book a ticket and then 'modify' it, this is +/- €12 to 15 per crossing. (DFDS for example) You'll be 100% sure of a crossing, though.
If you want to avoid queues for 100%, try the Newhaven-Dieppe connection or further away: Le Havre to Portsmouth. I found these connections on this map with all the routes.
I have traveled to Dover a lot, and my personal decision on what crossing to make would base on the time I would travel (peak season, super peak season with queues, or normal season). A queue of 3 hours is way worse than €5 to €12 extra costs! Dunkirk is in that case, the best move for now. (Until everyone starts doing that..)