Show me the Czech school that can train in English, has enough fleet and instructors for flying every day, and who charges T/O to LDG time! Alpha aviation? Come on, they train mainly on Cirrus, and their least expensive aircraft is Cessna Skylane! Imagine flight hour price...
The first thing that website price is always a minimum price, and it is never real. You should text and call, and talk. Don't sign the contracts blindly. And don't pay huge amount upfront. Even in the 'best of the best' school you can have some personal problems.
Of course all CAA/exam fees are on you. It is not 'hidden' cost, the good school usually just does not include them in the program. Ask the costs breakdown, any good school will provide it before starting your training. Also ask about so-called 'hidden' fees. The school will provide them as well, but you pay directly to the service providers (CAA, examiners, insurance company). YOU are a pilot, and you should plan ahead. If your school promises to pay those fees (with additional benefits like free uniform, free iPads, free books etc.), I am 100% sure they will charge you much more than the school that does not include those fees in the training program. Nothing is free, and nobody wants to pay external expenses instead of you. Just sit and calculate yourself, it helps a lot.
Actually in terms of price you should look on a flight hour price and instructor hour price. It is the main component, at least 90% of your expenses.
Landing fees. Yes, you should ask about them, and possibly choose another school that locates in another airport. Usually towered airports charge those fees, but it depends, the school can have agreement with the airport.
VAT. Again, show me the school that includes VAT in its quotation. Again, you should explicitly ask about it BEFORE signing the contract.
Instructors - from my opinion, one average instructor during the PPL is much better than 5 different (even good) instructors. Just because during the PPL you cannot evaluate them properly, but with more instructors they are just not able to track your progress. You will repeat the same things several times with different people. Actually it's arguable, every person makes a progress in his own pace, but the universal advice is "BE PREPARED". Prepare yourself as much as possible, and ask proper questions. Don't waste flight time on it. Be prepared BEFORE takeoff.
Plan ahead, ask as much as you can, calculate the costs, and don't pay upfront. Those tips work in any country, not only in Czech.
I found only 3 schools in the whole country that can teach in English, have enough fleet and instructors (i. e. instructor+airplane per students ratio), and have a reasonable flight hour price. Aviatickyklub, fly-for-fun and OK Air. All of them are out of Prague area. It was an advantage for me though: living expenses are less (cheaper rent), more calm area, more airports without landing fees around.
Personally I have experience with Aviatickyklub. I did my PPL for about 9000 Eur including living expenses and all fees (2017). Not extremely cheap, but I flew about 60 hours totally. And these hours still count towards my CPL. The school is good, but in 2017 they experienced lack of instructors in LKLN base. In LKRO it was OK. Their ground school was awful (mainly I had to prepare myself), but instructors are very professional and can answer all the questions. No landing fees in LKRO. Of course no any fuel surcharge. They have some mentioned signs of 'bad' school in terms of money (hobbs time, all external fees like insurance, exams etc. are on you), but I consider it as an advantage, not disadvantage. They provide a full breakdown before your training, and you can easily calculate. And they don't charge instructor time. At all. I suppose that I paid a reasonable price for my PPL.
I believe that for local it works a little bit differently, and it's possible to find a local flight club, fly enough hours, complete a ground school and pass exams and a check-ride. But the thread is about flight schools.