Things like this change according to the whims and fancies of the CIC and the VO. There may be precedence, but you cannot trust it. It could also be that you get a bad VO that looks negatively on this problem where as someone else gets someone more understanding. With this in mind this is what I think:
First, it seems that the VOs know that there is a problem with the FBI, and they seemed to have granted extensions generously. I know some people who have gotten a second extension after the first expired. So take it easy.
Second, always communicate with the VO if you are missing the deadlines i.e. ask for a second extension when your first extension expires. If for some reason you get a rejection from the FBI, send the documentation of this rejection to the VO telling them you will try again. If you face problems apply for state PCCs. These can be got much faster, and the VO would have some information, though it is not something they requested.
Finally, there was a case in this forum a year or two ago where the person got repeatedly rejected from the FBI fingerprinting. The VO seems to have waited for almost 6 months for this guys PCCs. (Apparently there were problems with the ridges of this guys fingerprints which the FBI did not like.) Finally, the VO allowed him to submit the state PCCs.
In the past few months there was a person who submitted the FBI PCC a month after the deadline, but without asking the VO for an extension. That seemed to have been accepted also.
So, please ask for extensions, and keep the communication open. I don't think you will get rejected for not providing the PCC in time. However, in the past the CIC is notorious for closing pending applications enmasse when a new system is in place. So if your application is pending for too long, and the CIC feels the Express entry system is going well, they can choose to close all of these pending application. You never know. However those getting it in the first few months of next year should be good.
