I am applying for a junior faculty position (i.e. tenure track assistant professor level) at a research-intensive US university this fall. As a part of the application process, the university asked for CV, cover letter, employment application letter, a list of referees at the initial phase. Now they have contacted me again and asked to submit three reference letters, a teaching statement, and a research plan via email in order to complete my application. Most interestingly for the reference letters, I have been given the options of having my references email them directly or I can forward them their letters. I can do whichever is more convenient to me. My concern is with the second option. If I ask my referees to send their letters to me, I can see what they are writing about me. Will they feel secured in such a way? Please advise how I should proceed in this regard.
You should ask your references to send the letters directly to the hiring committee. Your references will be more candid in letters that you have not seen and this will increase the credibility of the letters in the eyes of committee members.
Before electronic applications, it was not uncommon to give reference letters to the applicant in a sealed envelope with a signature on the back across the seal. The idea is if you do not trust the person you are writing a letter for, you probably should not be writing the letter. The sealed letter lets the hiring/admissions committee know it is confidential. There were/are also reference forwarding services.
That said, it is best if the letter writer forwards the letter directly. For the few old timers, they can print the letter and stick in an envelope. I have not been given, or given, a stamped and addressed envelope for a reference letter in a long time.
The one advantage of collecting the letters yourself, is you know they are submitted. This can be overcome by following up with the letter writers to make sure they have submitted the letter.
I know different places have different customs, and especially when people leave a position, they will often get reference letters to take with them so their former boss does not need to continue writing references ( rather lazy... in some cases I know people were even asked to write the letter themselves...)
If the University asks for you to choose one or the other... I'd go with having the referees send them directly. A direct reference is more reliable (because it can be more candid and you'll never know) but I suspect they probably allow the indirect one because some people will just have the letters and don't want to or cannot ask another favour of the referee.
Meaning: I'd regard the "you can send it yourself" option as a fallback only, for cases where the other one does not work.
The best way is you send your latest updates to the referees and request them to look into the updates before sensding the recommendation letters. Though sometimes many applications ask for open recommendation letters where the referee send/gives the recommendation letter to the applicant and the applicant finally attached them to the application, but your case is different to it. So have faith in your referees that they have given good recommendations for you.