They will look for items of correspondence which could directly (or through a chain ) lead back to the waste producer. The licenced Waste Carrier is only part of your responsibility; you are also responsible that the waste ends up in a licenced Waste Management facility, regardless of who transports it there.
I can't speak for EA, but SEPA are very proactive and not just reactive. But I can only comment on B2B, however, I do suspect domestic producers (i.e. private individuals) would not be pursued unless they are involved consistently.
As for the OP original question, I would say it is quite simply down to money. Whilst greed will form part of it, when you consider that a Waste Management Licence for a medium sized facility can be £18,000 per year upwards (payable to SEPA (I'm not sure about EA fees)) along with all the other costs for waste separation which involves both excavators, wheeled shovels, trommels, fines refiners, picking lines along with the staff for them, reasonably sized land to store the various materials, crushers to turn the rubble and brick into 6F5 etc. Well, it's not a cheap operation to set up.
If you want to just take all the waste straight to landfill, well just looking at an 8 yard builders skip which can cost £170+ it can hold over 10 tonnes of weight if there is a lot of rubble or soil in it. Taking into account landfill tax is about to go up to £96.70 per tonne and rather unfairly VAT is charged on this tax (ridiculous if you ask me), and the net which goes to the landfill company can be around £20 per tonne. Essentially you can be looking at £116+ VAT per tonne to landfill waste, so you don't want to be taking rubble, soil and other heavy items like wood to landfill - but to separate waste you need a Waste Management Licence plus the setup as detailed above.
Typically, however, an 8 yard skip will hold an average of around 3-4 tonnes of waste, but if that's all sent to landfill then the skip has made a loss. They need to either take it to a licenced recycling facility which will charge roughly £110 to dispose of (unless it's full of crap upon which they may be charged a tonnage rate and screwed) leaving about £60 to go towards haulage and overhead costs (for the skip hire company) or they fly tip and make a lot more money.
I would find it unlikely that a skip hire company would fly tip, it's more likely the flat beds and caged vans, which are more likely to be unlicensed and without livery. Skip hire companies are more likely to find larger scale ways to avoid landfill tax of which there are quite a few.
