You wish to maintain FireWire connection and to be able to boot from external storage—yes, I know that this is the 68K MLA—make sure that the bridge to internal devices is mediated by an Oxford chip and not a Prolific (which is by far the commonest in gear coming out of Asia).

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I have 3 enclosures - a 2.5" Oxford911 based one, a Initio-based hard disk case and a 5.25" DVD-RW case with a Prolific chipset. All boot fine. I think you may find only early Prolific chipsets, and maybe older Macs, have that kind of issue - later ones (i.e. from the last 2-3 years) don't AFAIK.

The way to check what chipset is used its to look in the FireWire section in System Profiler when the drive is attached and powered on. There should be a 'Manufacturer' property for the device that tells you the vendor.