After watching the Destroy ending again, I can say you are right. This only affects the Destroy ending, though, since with Reaper knowledge Shepard and all the species could've rebuilt the relays anyway (if they were Reaper inventions, but I guess this is another discussion).
The only explanation I could think for this is that they wanted to give each ending similar value. Since Destroy was generally considered the only "positive" ending (and not because of the Indoctrination theory), they couldn't simply make a 180 turn and make it the only ending where galaxy doesn't prosper after merging with/controlling the Reapers.
Actually I just read that in the EC low EMS Destroy ending, the relays are completely destroyed, and with high EMS they aren't, which means they simply added that bit and rewarded the player for doing good in all endings. The breath scene is not included in EC.
I couldn't find a quote, but users at Bioware forums agreed it is canon and all ME editions released after EC came out will include it.