I think one consequence is that there won't be as many uncirculated bills pushed out as now when the polymer notes come out. After Australia switched its $100 to polymer, they printed large quantities in 1996 to 1999, and didn't do another print run until 2008 (a 9 year gap). However, they use denominations from $50 downwards very frequently, there's still a steady flow of new notes being issued. In our case, we might be seeing Macklem/Carney $100s for a very long time even if either one of them is replaced during the lifetime of the series.
The benefit of polymer does reside mostly with the low denominations, and other countries generally do the low denominations first in the transition to polymer. I think that the BoC is starting with the $100 to ease the transition for the public, as it's a less used note, and banknote handling equipment/ATMs will have a little more time to iron out any problems with the new notes.
The transition won't be without hiccups, if you've seen a full bundle of polymer notes before, they're about 1/3rd less thick than a bundle of $5 notes now, and counting machines will need to be adjusted for the thinness of the new notes. Banks in Australia also don't load consecutive brand new notes into ATMs even up to today as they tend to stick and cause jams in the machinery. They have to shuffle up new notes into circulated notes to guarantee that ATMs will run smoother.
Banks will also have to be vigilant in taking notes that have any tears in them, as they rip very easily once a cut is initiated on the note, possibly causing problems with note handling equipment. (I'm sure I'm not the only one to have gotten torn notes from the bank and ATMs). Even the central bank in Australia tells banks not to use elastics to band notes as they will cause the border to stretch, nor paperclips as they may cause the printing to scratch right off.
As for reading the notes, I heard the machine readable features is hidden within the ink located on certain parts of the note. (US notes contain magnetic ink in certain areas of the notes for machines to read them)