Not mean to be discouraging.
"去年毕业时，intern时的大老板对我说现在没opening , 今年初有人退休，可能招人，说我是top-notch. "
-- From this sentence alone, it really doesn't mean anything. It was nice that you gave him a positive impression. Unless you were a super intern who outperformed experienced employees, a big boss wouldn't treat you significantly different.
"大老板是Hiring manager 的boss, 这次不在interview panel里，很不正常."
-- It is perfectly normal. It is a junior position. The boss of the hiring manager is usually not involved in such hiring process, unless it is a small start-up, like with 15 employess only.
"也不知道Hiring manager 让我面试 是否只是给大老板 或我一个面子而已，并不打算招我 (通常只面3-4 人而已)"
-- That might be one reason. Most possibly, it is due to your experience as an intern there. If an intern does well, a company would like to give her/him a higher priority in hiring. Interviwing is hard. It is normal that a good interviewee turns out to be a bad hire. So it is a safe bet to hire people you already know and worked with. Another factor is professional courtesy. It is considered very mean to not even give an interview to a good intern, if the intern is local.
"刚听说大老板在面试期间计划休假，我和原公司的好友都觉得他是故意回避. 因为雇我会得罪政府部门，不雇我，以后还需要常和我联系，比如我月底就要去audit原公司， 大老板接待"
-- No offense. You and your friend over-evaluate yourselves. One couldn't become a big boss if one doesn't know how to play the game, especially one has to deal with government. Believe me. The hiring is the least of his concerns.
"不知道Hiring manager 和大老板是怎么想的，以前大老板对我不错，9个月的时间可以改变很多事。"
-- Nothing changed. You over-think. The big boss acts very professionally. Nothing unusual.
The primary consideration are what is the relationship between the company and your department. They work closely, but how closely? What is the relationship between your boss and the big boss? If you are hired by the company, will your current manager care?
If your current manager may get irriated, the company wouldn't hire you no matter what. They will give an interview, which is a good opportunity to strengthen a professional relationship, both for you and the company. It is a different story for you, though. If your current manager heard of your interview, it is not a good thing. It is a small world. In your case, most probably it would happen due to the close relationship between the company and your department. If you are not sure, the safe bet is not to take the risk. Don't worry the low salary for your first year. Pay attetiono to learn and improve your skills, which is the long term investment strategy.
If you can easily find another job, it is another story.
