For my personal car i use both methods. For larger chips i still go the old school route i.e. fill, sand and finish. For smaller chips i use the Dr ColorChip method. I agree with Mike's opinion that my old school method is better in the final analysis but it's costly on time. Building up that slight "bulge" with numerous thin applications with OEM paint and then isolating the sand down to just that bulge is a meticulous effort and takes time to do right. I will happily say, though, it yields far superior results and yes, on my metallic flaked paint. Dr. ColorChip is fast and much easier and does an adequate job of hiding the smaller chips.
Again, for me, it comes down to the size of the chip. If i had a customer car i would talk them into the DC approach and caution towards the results not being perfect but much better and gauge their acceptance. If they wanted my meticulous approach i would price it out with the additional time that takes.
Just my opinion...