Pyramid Match Kernel: How to fit grid around data points?
No, that's not it. Look at the last sentence of your quote:


  ... which may be enforced by scaling the data to some precision and
  truncating to integer values.


So this is exactly what you do. Take all your feature vectors, multiply them by 1000 (or some other factor), and truncate to integer. Then the distance between any two unique feature vectors will have to be >= 1. If you have a new vector y, then you multiply it by the same factor and truncate.