There are a few issues with that question. None of them insurmountable, but until these issues are fixed, this question will continue to yo-yo between open and closed.
As written, it's Non Constructive. To wit:
As it currently stands, this question is not a good fit for our Q&A
format. We expect answers to be supported by facts, references, or
specific expertise, but this question will likely solicit debate,
arguments, polling, or extended discussion.
Your meta question asks, "What tools can I use to X?" That's skirting the line of polling. If your question on Stack Overflow is actually asking that, then it's not constructive. See also: Q&A is hard, let's go shopping!
The next problem is that you've given us an overly broad question, simply
I would like to know if there are some better way to help understand
the PDF format when one read its specification. For example, do we
have a pdf editor which can show the difference in raw data when one
execute an operation?
"Better"? "Understand the specification"? There's a wide range of content in there. I'm sure entire books have been written on the subject. That's what the FAQ says, If the canonical answer to your question can fill a book, it's too broad.
We need specifics, we need context, we need to know what problem you're solving. Is this just a fishing expedition? You're curious about this and so you've decided to ask Stack Overflow? Or do you have a task to parse a PDF file? The answer to those questions gives us context and lets us know the actual problem you need to solve.
Finally, some of the answers (ok, the vast majority of them) are
link-only answers. That's normally an indication of trouble in the question. It's a herring, though not necessarily a red one. Just a stinky one.
As it stands, this would probably make a great blog post, but not so good on the Q&A side of things. I would have voted to close it as well, given its current state.