How much more detail do you need? Simply put, the cause of the collisions are not considered which then compromises the integrity of the evidence by scientific standards. As stated in the following link, "Researchers have a responsibility to take account of all relevant evidence and present it without omission, misrepresentation or deception."
http://www.respectpr...e/cstds.php?id=
... unless of course physicists are above such standards. Then of course everything is just fine and dandy.
"... you should rather ask if the quarks are well aligned, not the protons." - if they can't align the protons, they assuredly cannot align quarks.
I think the work they are doing is very very important. All the more reason why they should get it right by considering all possibilities "without omission". This has nothing to do with stupidity. It has to do with the effectual methodology of the art of physics. Physics is the practice of how observed or measured effects cause other effects, not cause and effect. So it makes perfect sense for physicists to focus on the effect of collisions and their effects.
However, the inherent problem with effectual methodology is that it is incomplete by not taking into account the cause of the effects measured. "Choosing to" ignore this fact ... now that would indeed be stupid. If I am not mistaken science is about discovery, not dogma. If something comes up that has not been considered before and has a fundamental impact on the art, then it is the responsibility of the practitioners of the art to address it, not ignore it. To do otherwise lowers the high standards we come to expect of science.