Well, audio that comes in over SPDIF or lightpipe(the ISA428) does bypass 003 converters going in. Does it sound better? That's a question you ust answer for yourself. Does the 003 sound better when clocked from the ISA(or any external) clock? Once again, you have to make that decision. For me, I was never certain I heard a significant improvement, no matter how I clocked my 003 setup(including clocking via a Lucid GenX 192 external clock).
At the end of the day, I am way more interested in a decent recording of a great performance of a great song. That is more desirable(to me) than a perfect recording of crap
I felt a more certain improvement by moving all my work to 48K over 44.1K(but, YMMV). Also, choosing the best combination of mic and preamp matters more than using "better" converters("better" often being subjective). That's one reason I really liked the 428/003 setup as I used those 4 extra line inputs(on the 428) to patch in a pair of Neve clones and a pair of API 312 clones. Vocals thru the 312 was clearly better than even the ISA preamps, as was guitar/bass thru the Neve clones. BTW, I still have my 428 today and it handles overheads, ride and hat mics in my drum room