Honestly, I feel like there are few flaws that prevent it from doing its job. The first is the omnipresent Heatran which comes in on Sacred Fire and laughs. This is one common weakness it has with its supporting Pokemon like DD Mega Charizard X, Dragonite, and Salamence. It's worn out very easily as its weak to every entry hazard. Sand and U-turn damage can wear it out even faster. Mono Fire-typing is a good and bad. Being weak to Ground-, Rock-, and Water-type moves is problematic, but Fairy-, Fire-, Ice-, Steel-, and Bug- resistances are good. Your playing Entei for Sacred Fire and that alone. This means that Entei has only one niche: nuke that can burn common switch-ins. Entei is very niche, but it's not outclassed. These reasons themselves make Entei a B canditate. It's not partially outclassed by anything like the definition, but these flaws keep it from doing its job consistently. "Spreading burns" doesn't always happen. It's only around a 45% chance to burn (accounting its accuracy) and its PP can be easily stalled out (8 PP). If it gets 8 Sacred Fire's out, that would be amazing, but lets not go to things like "oh Garchomp is safe switch-in, oh wait, Sacred Fire burns :0". I am nominating it for solid B+ Rank especially since it fits the B Tier definition better than the A.
These reasons? No, I don't think they do at all. Heatran fears Bulldoze, and cannot switch in safely. Entei can eliminate this counter easily.
Furthermore, I've stated in the past that I believe that spin/Defog support falls under team support rather than specific support that you have to bother with for one team member. While being weak to Stealth Rock is certainly a con, it shouldn't have a large impact on the ranking of a Pokemon. Sacred Fire is difficult to PP stall, as well. What exactly is going to be taking those hits? What's stopping me from predicting and using Stone Edge instead?
The rest of the stuff you wrote (after the bold) isn't really an argument. Entei might not get to do its job. Stealth Rock, sand, and Spikes might be up. You might not have a Defogger. Sacred Fire might not burn. We're not going to drop Deoxys-S a tier because it might not get two layers up.
Entei has one role, and it does it reliably enough to be a prominent threat.