As far as I can tell (only from the abstract though) this study is simply saying that the ratio of LDL/HDL didn't show much difference than a simple TC/HDL measurement in terms of predicting a coronary event. Keep in mind this is a cohort study meaning that it is observational and not a randomized controlled trial. This leaves it vulnerable to bias and uncontrolled variables. You can only really detect correlation rather than causation. For example, you find ice-cream sales are associated with increases in outdoor temperature. During periods of increased outdoor temperature there has also been found to be an increase in drownings. From this observation, you could hypothesize that increases in ice cream sales are associated with increases in drownings. In this paper higher TC/HDL and HDL/LDL ratios are both associated with increased risk of a coronary event. It doesn't say that LDL particle does not.
Check these studies out and give them to your doc:
This is a study out of Berkeley talking about how pattern B LDL vs Pattern A is more dangerous (meaning small dense LDL vs normal larger LDL):http://www.lbl.gov/Science-Articles/Archive/cholesterol-particles.html
MD's are usually skeptical of anything that they cannot influence with drug therapy. There is no drug that can make your LDL particle size change, so they do not put any value there even if the research points otherwise.