The trash bytes are unique to the device/rom that generates the pokémon, since they are just what lied in memory when the pokémon was generated (from my point of view I don't see a reason why they didn't clear those bytes, but at the same time, I also don't see a reason why they should have cared).
What I said about Colo/XD removing them is from this point: OK, we know we can't never do 1:1 replication (since that needs the actual distro device, or a copy of it), but if we throw trash aside and just concentrate on what makes the pokémon unique to that event (PID, TID, OT, OTgender, IV, level, met place...etc) and we can replicate that 1:1 that would still be awesome. If you are using a homebrew app to get them I'd personally still prefer single pk3 files from people who actually got the event.
But for personal use? Fun? Gen 4 onwards (since that clears the trash too)? I'd really like to have something like that, albeit I understand the concerns collectors may have, but faking some gen 3 event on gen 4 onwards is really difficult to discern (and many are available anyways).
That's just my personal opinion, actually I think the fact that we can't replicate trash is good, because A) Doesn't matter for gameplay/gen 4 onwards B) It's a good way to quickly know if the pk3 file was just generated C) There's a legit way to get rid of the trash bytes so even generated pokémon can be claimed to be fully legal without having trash bytes.
ps: I think I finally found a way to tell legal from legit appart (I always confuse the correct word), hope I didn't mix them up.
ps2: yes, GF switching to an in-game generation for most events is really nice, gen 1-3 are a nightmare for events....and gen 3 is actually better than those.