Ksus,
I think the answer to your question depends on the company doing the hiring and to a large extent how difficult they view the whole security check process to be. ACA for instance were prepared to interview aliens although they would tell you that in order to be offered a class date you would have to wait until the security check system was working. For some this meant a 6 month wait and for others it has meant an indefinite wait.
On the other hand, I know one of the other big regionals that will ask if you have a US passport during the telephone pre-screening. If you answer yes, no problems. If you answer no, you won't get a follow up call for an interview. Now I know this compny has a lot of foreign nationals working for them. So it's not a problem with aliens, just that they are not prepared to waste time interviewing people they can't offer class dates to. I can't say I blame them.
This whole system, while well intentioned, doesn't seem to have been thought out well enough. I'm all for keeping the skies safer, but it doesn't seem that smart to say that you want pilots to have security checks, but not tell them how to go about it.
Kenny,
