maybe you posted to Canberra embassy but Sydney consultant its been like that for years. Nothing new, the reason you got it all sent back is you didn't do it online like they ask. Like I said follow the instructions and you will be fine.
you have always if applying to the Sydney consult, had to apply online and wait for them to approve and and receive an email, saying send your stuff lol If you follow the instructions there should be no problem. The visa itself is a invite to visit Thailand. This is nothing new.
Your not the first person to overstay, but never advisable to do, but you will have to pay the fine at the airport as others have said 500 a day. Then you will be in the hands of the immigration officer when you return, would be my guess.
Well if that's a serious question? then they are 2 seperate things lol first you need to get a retirement visa and then get a multi entry permit lol then you can re-entry as many times as they both valid for lol.