Well, I think, it's a more 'realistic' approach but it does lead to the problem that you get lots of low-level items (which will typically get sold at the first opportunity).I can definitely see why using CR would be a problem... you end up with a bunch of low level gear from what was supposed to be a level-appropriate encounter.
Imho, if there's a huge difference between CR and EL the encounter tends to be far easier than a level-appropriate encounter. An encounter with 40 CR1 creatures may have a high EL but it isn't difficult at all. So, I prefer a treasure consisting of a large number of low level items to a single powerful one.
Actually, if you care about treasure composition for an encounter you probably won't use the random method anyway.
For intelligent foes I tend to select at least the most powerful items and only roll for the low-level stuff randomly (if at all).