This behaviour makes perfect sense per the fare rules.
Remember the pricing is not a combination of two segments, but an overall fare between the two points. If the flight you pick or are on only has Y, then Y is what you get booked into, but if it has J, then great J it is... but the price is the same. You're purchasing CBR-NAN as a fare.
I've seen this in other instances, for example I recently booked a NZ J fare to the US involving a regional sector that has, like CBR, both single class CRJ and two class flights - pricing out exactly the same no matter which sector.
Essentially these tag flights are considered a component of the overall fare, and as long as they fit certain criteria of routing and (sometimes) zonal restrictions (for example, if you wanted to do CBR-ADL-PER-SYD-NAN...) those sectors are more or less "thrown in at a nominal cost.
Now as you say it's a one way street in respect that you had that fare instance where you were booked into Y, but wound up being changed to a two class a/c and they would not put you in J(or credit it) even though, in theory, they should have with no charge but once ticket is issued that's how it is.
I still don't by the line given about flights between CBR-SYD being put as flex Y - it may be in practice due to the large number of Dash8's on the route, but they absolutely should, and will, book into J on a two class service. I will stay confident with that assessment until i see something specifically in writing (ie: fare rules) that specifiy otherwise