I don't see why that would be a problem.  I'm assuming they'll issue the engine number to the vehicle with your Burb's chassis number.  When the two coorespond, you should be good to go.
I would obtain guidelines on the stamping of the block from the RTA, just so you have no probs.

Andy,
It is clear that your blue slip guy does not have the slightest idea what he is doing.
Do not attempt to just put a number on it yourself because there are guidlines on what format, size, location correct figures etc. and if it is not done correctly RTA will reject it.
Go and see another dude that knows what he is doing.

Give me a call if you get stuck.
Cheers and Merry Christmas

Chris.

I went to the RTA today  I have booked in to go to there Botany site to get the engine stamped on Jan 7, so as much as I dont want to wait that long, at least I can register it the same day (I hope!)

Chris, the guy is ok, its just he was very busy and didnt explain the process well enough, it all seems to make sense now, although he should have organised the rta stamping for me but he had 5 people standing behind me waiting, so I had to do it instead of him! I think thats what he was going on about, he still had to give me the blue slip with everything else ok then I take it to the RTA to organize for a Engine number! You can do it that way!

January 7 - D'oh!