Great Britain representative Muhammad earned bronze while top seed Cook bowed out in the early stages, but the London 2012 bronze medallist has insisted that they can still challenge for top honours in Rio de Janeiro next year.
The 24-year-old told reporters: "When both of us are in shape, we are some of the best fighters in the world.
"Even if I don't see eye to eye with him sometimes, I have respect for him. Every road goes to Rio from now on in. Every point counts for qualification for Rio so it is a massive bonus for me to get some here."
Muhammad earned selection for London 2012 ahead of Cook, which resulted in Cook switching his allegiances to Moldova ahead of Baku.