I don't think you can boot from the compact flash - the drivers need to be loaded before it can be accessed.
I have an external slimline CD-ROM drive for one of my Amigas, in a custom case. It is nothing more than a laptop drive with a 2.5"-3.5" adaptor and a PSU (and a 3.5"-2.5" buffered interface). It came from Power Computing and included the IDEFix '97 package.
If you want to fit your own, remember that most laptop CD-ROM drives don't use standard 44-pin interfaces - they might be 44-pin and conform to the usual standards (I've never checked), but the socket is usually different. Having said that, it is possible to get slimline drives with standard 3.5" interfaces - our Dell server at work has, somewhat inexplicably, a slimline CD-ROM drive.
Amiga dealers tend to recommend buffered IDE interfaces if you're using more than one drive, because the unbuffered 1200 IDE interface essentially connects the drives directly to the CPU. The theory is that this can potentially cause serious damage to the CPU, killing the computer.