I know how you feel. I went from a D1 --> D4, and the difference is pretty big. Most of these differences are due to the fact that the D4 has a locked bootloader, while the D1 did not. Fastboot files are the firmware files that you flash with RSD Lite. Unfortunately, unlike the SFB files which (as far as I could tell) you could always flash no matter what (very very difficult to hardbrick a D1) you have to be more careful with fastboot files. That is the reason why you have to be sure you want to flash the ICS leak, because once you do, the Gingerbread fastboot files will no longer work. I haven't seen a definitive answer as to why this is the case, but I believe it has something to do with Motorola changing the partition sizes in the ICS update. This implies we may one day gain the ability to fastboot back to Gingerbread, but nobody has figured that out just yet.
As for Safestrap, it is a ClockWorkMod recovery, so in some sense it IS CWM. That being said, there are some important differences. What Safestrap does is it sets up your phone to dual boot. It labels these two systems 'non-safe' and 'safe'. Your 'non-safe' system is the stock system, and safeboot will allow you to back this up, but will not allow you to flash any ROMs/Zips to it. Your 'Safe' system is the system Safestrap allows you to flash zips (ROMs) to. The upside to this is that if you softbrick your phone, you can just switch back to your 'non-safe' system and be fine. The downside is that this does take up some space on the internal memory card, which is a bit inconvenient.
One mistake many people make when flashing with Safestrap for the first time is forgetting to do a factory reset on their safe system before flashing the first ROM. Apparently you have to do that first, or you will soft brick (recoverable via safestrap easily). Honestly I was very worried at first, since when I got the D4 there weren't any Fastboot files, but imho it is actually better than what we had with the D1, minus the ability to easily boot custom kernels. I have a "to play" ICS ROM loaded up, but when I NEED everything to work perfectly, I can jump back to stock in a few minutes. (Not that the ICS ROMs we have aren't good, they're pretty awesome).