For the sake of logging time for ATP, the flight needs to be at least 50 nm away from the point of departure, but does not require a landing. An example of this would be something like search and rescue flying--take off from airport A, fly all over the place, then land back at airport A. There is no allowance for a flight of less than 50 miles.
For the sake of meeting the Part 135 time requirements, a flight only needs to have a landing at another airport to count as cross country, no matter how far away the airport is. For instance, there is a small airport 6 miles away from the larger airport that I teach out of. If I go into that airport for touch and goes with a student, the whole flight counts towards the Part 135 XC minimums.
As far as what your instructor was saying about logging time after the commercial certificate, he might have been wrong, or you might have misunderstood. Time is time, regardless of the certificate you hold. However, cross country flights towards the private, instrument, and commercial certificates must have a landing at least 50 nm away. So it would be confusing to log all of the "Part 135, less than 50 nm" flights as cross country. When you go for your commercial checkride, you'll have to dig through each entry and figure out which flights were over 50 nm and which ones weren't.
After getting your commercial license, you'll probably be looking to meet the Part 135 minimums, so some people start writing any flights with a landing other than the point of departure as cross country. I prefer to do that in my electronic logbook and only record the 50+ nm flights in my paper logbook for the same reason I stated above about going for the commercial checkride--when I go for my ATP, I don't want to sort through a bunch of little 10 mile hops logged as cross country time that do not count for ATP.
I don't have time to break it all down into specific regs, but all of this is based on Part 61.1(b)(3).
