I'm planning on facing this with CleenROM myself if time permits this weekend, so please help me understand.
I think I recall that Setup (HTC app with top hat icon) runs at startup after the factory reset. I can completely skip the Gmail setup? I believe that triggers the Market connection and download.
I can skip that and then rerun Setup by hand after changing my other settings?
So you're suggestions worked, my old apps did not auto download. There may be some refinements/simplifications to my process as, in paranoia, I may have turned off unnecessary settings. But for starters, here's what I did...
Factory reset and full wipe.
Flashed CleanROM 2.1. It then boots to the startup/setup program...
I was unable to get out of this program, so I went through like this...
First screen, "Scheduled sync": I chose "manually sync", and then "next".
Second screen, "Set up WiFi": I did this, and then "next".
Third screen, "Use Google Location": I let 'em have it, and then "next".
Fourth screen, "Set up accounts": I did not set any up at this time, and just pressed "next".
This transistioned to the home screen and no apps proceeded to download.
In "Settings" then "Privacy", the "Automatic Restore" was checked. But this line was grey'ed out so I could not uncheck it. For now I left it like this. (***see below. I later noticed something that could be tried here)
In "Settings" under "Accounts and sync", I unchecked "Background data", then it asked me about "Backup and Restore", I unchecked this (or left it unchecked, I don't remember), then pressed "Next" and then "Finish".
At his time, Android sync'd my contacts. Still no apps.
Then, still in "Accounts and sync" settings, I checked "Auto-sync", and the rest of the Google accounts stuff, sync'd (mail, calendar, etc).
In "Settings", went to "Privacy", and both "Back up my settings" and "Automatic restore" were checked (?), and I was able to uncheck them both.
***This is when I noticed that if you want to uncheck them both, you have uncheck "Automatic restore"
first, and then uncheck "Back up my settings". The other way around leaves "Automatic restore" greyed out and nonresponsive.
So there you have it, the auto-download was never triggered. Although I'm still not sure which step was key. In this sequence, at some point or another, it seems that all of the relevant settings were "on". Perhaps, you're right Early, it is the initial setup program, which automatically runs after your first boot, that triggers the auto-download. And since I didn't establish an account at that time, nothing happened. So you "Finish" that program, and go on your merry way. And maybe none of the "settings juggling" I did afterwards was necessary.