Flashing a new ROM indeed resets it to an uncustomized state.
Over time, I've probably created hundreds of black holes - I use all 7 home screens, including using apps and bookmarks inside of folders. Ugh!
The good news is that things are getting easier all the time - and I'm getting a little smarter at it too. (I'm only creating red giants or white dwarfs now).
Here's a case in point: Froyo-based ROMs. In Android 2.2, Google has furthered the concept of what it means to be a "cloud phone" - if you turn on an option to do so, you can back up all your "Settings" to the cloud - so that if you get a replacement Android phone with Froyo (or load a "blank" Froyo ROM), the first thing it does is to "sync" all of your apps and Android settings back to the phone, without requiring any user intervention. Power the ROM up, sign in to your Google account, put the phone on the charger & let it sit for 10-15 minutes - and all your apps, settings and bookmarks are restored from the Market.
And if you are using a non-Sense home "Launcher" (e.g. ADW Launcher), you can back up all your home screen layouts and launcher settings to your SD card - just restore them in a couple clicks. Same thing for "CyanogenMod" settings.
It's not completely perfect, but it's a lot better than it was in 2.1 - and it also partially removes the need to screw around with apps2sd. I would estimate that now I am only spending 15-25 minutes of "face time" duplicating the behavior of a prior 2.2 ROM, and perhaps a total of 1 hour elapsed time. It won't restore application settings though - you need to either do that manually, or figure out how to make Ti Backup work for you in that case.
I don't want to over-sell it though; it's still nowhere near something like a "1 click full restore".
eu1