It shouldn't have an impact on your PR application, but I am aware of at least one person, who applied Family Class inland, who completed their PR application but was told to fill out an online declaration form confirming they are in Canada to complete the process. They cannot, because they are not in Canada. They cannot get back on an airplane to come to Canada either.
This is just a possible outcome, though it isn't completely applicable in your case since I don't believe EE are doing the portal confirmation (they may be and I may be wrong on this).