Atomik, there is a big difference between websites such as SkyScanner and Kayak which could be described as flight comparison sites and WebJet which is an online travel agent.
Flight comparison sites direct you to a range of online travel agents (whose HQ could be based anywhere in the world). You then book your flight and make payment to the agent offering the deal.
WebJet is a travel agent based in Australia. The fares you search for are booked through WebJet and you make payment to Webjet through their website.
I have used SkyScanner often, especially when I lived in UK and they were great for finding the best EasyJet / Ryan Air / other provider for short duration flights from UK to continental Europe.
Your post prompted me to try a Kayak search. I searched for flights to London from my nearest capital city. Many of the search results offered where through internationally-based travel agents. Kayak returned many results from eDreams/Opodo whom I would never book through after a bad experience with them earlier this year. They are so dodgy. I'm not going to begin about my experience with them but any web search of eDreams / Opodo would reveal how untrustworthy they are. Here's one such link:
http://www.which.co.uk/home-and-gar...which-travel-investigates-opodo-and-edreams-/
My point is, if you are booking long haul and expensive flights around the world, I would want to book with a trustworthy and locally based travel agent. Going for the cheapest fare, may work for some, but I would rather pay $200 extra for the piece of mind of booking through a trusted locally based agent.
(In my search there was one fare that available to book through kayak.com.au (who are a US based company owned by the Priceline group) amongst all the eDreams results. This was $270 cheaper than my Webjet. I would choose Webjet!
(20min delay)