I did have to fill an online app at TSA. Later the DOJ determined that since I already have a type rating I was elegible for expedited process and the online request was cancelled. I was granted training approval 7 days after expediter request. TSA was very helpful throughout the whole thing.
On the other hand at Mesa, they make everybody sign the DOJ disclaimer on the interview. They seem to do it by themselves. I was not given any info on anything, I even had to make them aware of the fact that I need to get DOJ clearance.