I would say for the average Joe it doesnt make so much difference. But when we are talking about people who use technique in Gregorian Chant and use the semiology it is important. Honestly, a lot depends on the "school" of Gregorian Chant. There are many different theories. So, it depends on what your project is for- who will be using it.

I would second what Royce Nickel wrote, and stress the importance of paying particular attention to the elongated virga, which is sometimes neglected by the Triplex and Novum copyists. With that said, you ought to consider copying from the manuscript facsimile itself rather than the Novum, as there are errors besides the long virga. Examine the introit Protector, GN 1.310. The copyist fell into the same error as the Triplex copyist and wrote a punctum for the last note of melior. It may be excusable if only the Paléographie musicale were available, but we now have high quality scans available for free online. The high resolution image reveals that the note actually appears to be a faintly written uncinus, and comparative analysis with the same figure elsewhere confirms that interpretation.
Have you made any of your duplex or triplex editions available online yet?

I'm not sure if Gregorio has the elongated virga though.

viS, cf. vipp2su2