Sorry for butting in--I'm not a normal part of the crafts forum, but was lurking and I know the answer to the question. The issue is that any aftermarket products alter the seating of the straps, how far away from the plastic frame of the seat the baby sits, etc. The testing that is done on any seat is done with that seat EXACTLY as shipped, with (or without) strap covers, etc. The big problem with aftermarket covers is that they are typically a different thickness or softness than the original cover. That means that in a crash, the new cover will compress and shift in a different way than would have happened with the original cover. This could theoretically place the child in danger. The worst-case scenario is an aftermarket cover that's very soft and puffy (which is often exactly what parents want). The parents put the baby in the seat, often in a nice soft puffy snowsuit or coat, and in order to fit everything in they have to loosen the straps. They tighten the straps enough to look and feel correct, but in a crash the soft cover and the soft coat compress, making the straps suddenly very loose. The child can experience much higher crash effects or even "squirt" right out of the straps in that (extreme, but possible) situation.
Knowing the physics of it, I think the least dangerous but still cute cover would be one with NO padding, just the thickness of a bedsheet or something. However, car seat experts have a blanket non-recommendation of ANY aftermarket products (including sheepskin or padded strap covers, those little head stabilizers, any Bundle-Me-type "coats" that are any thicker than microfleece, etc). For the same reason, they strongly recommend against puffy or padded coats or jackets.