It's a pain isn't it!
Multiflight are one in particular I find really irritating. They flash low prices about all over the place (here included). But when you dig deeper they aren't any lower than average. MCC is a good example. Why quote an ex vat price, we all have to pay it.
Guess it's just a case of you doing your research properly - don't be scared to phone up and ask!
One other one to look for is how schools charge for hours flown. Some are airborne +15 mins (10 for pre take off stuff and taxi/hold etc, 5 for after landing). Whilst this works out well if you are training at a large busy airfield (Leeds for example), be wary of smaller quiet airfields where you won't spend anything like that amount of time on checks and holding. The one that springs to mind is Perth.