Though "without prejudice" does mean what the dictionary says, and bdb's example of a claim in the wrong court being dismissed without prejudice (meaning the claimant is free to refile in the correct court, whereas without the phrase a dismissed claim could not be refiled) is a good one, it is not a magic spell that allows you to bypass the inconvenient bits of the law: despite what you read on the internet, there are remarkably few such incantations, or at least effective ones.
'Without prejudice' is typically used in settlement negotiations, where you might suggest "We will admit our client is at fault, if you agree to limit the damages to the actual repair bill". Obviously if the negotiations break down it would prejudice your case that you are not at fault if this letter could be made public, and equally obviously it is in the public interest for such negotiations to settle cases before trial if possible; so your letter is marked 'Without Prejudice' (to our public assertion that we are not at fault), which means that the letter cannot be put in evidence. The law on without prejudice communications has been pretty well codified in most jurisdictions, and neither putting the words on a non-confidential document nor omitting them on a confidential one will actually affect the outcome; but lawyers never like to leave out words where they might be useful.
It looks from your quotation as if Mr Prybylko has extended this interpretation further than it can reasonably bear (and also misunderstands ellipses). "'Without prejudice' [means] that you reserve the right to modify or amend the agreement of the contract"; well, no it doesn't. If you propose a contract on certain terms it is implicit that either the other person agrees (and you both keep the terms) or he does not (and you may suggest changed ones); "Without Prejudice" does not affect this. Similarly, if you try to keep the words in a final signed contract, any competent lawyer will strike them out as surplusage; unless you specify without prejudice to what and why, they are meaningless and can only make the contract less useful.
There are other contexts where the phrase can helpfully be used, such as accepting a payment without prejudice to your ability to sue later, which is the opposite of "in full and final settlement"; but simply marking all documents 'Without Prejudice" will not save you from anything but the respect of lawyers.