Following along in the same lines as before, the question becomes have I modeled my HQ wrong or have I done it in such a way that it's not the "best?"
Short answer: No.
Not unless you've given him a weapon he clearly can't have or something along those lines and even then, you may have some leeway depending on who you're playing against.
Since we know that how you paint your HQ will affect how he is perceived, we should also add that how he is modeled will do the same thing.
How modeling larger than life can be good
This is my favorite. I do this all the time. In fact, I took my HQ, the very one seen up top and ripped him off that base to put him on a bigger one later on. I wanted him to stand out even more.
By modeling your HQ to seem bigger than he really is, you're doing the same thing creatures in nature do all the time when it comes to fighting. They posture to make themselves look more dangerous and seem more deadly to their opponents.
There are times when just looking tough can be enough to save you from getting in over your head. If your opponent looks at your HQ and sees some ornate armoured model standing on a rock outcropping with a huge banner depicting his many wins with tons of skulls at the base of his feet... he may decide the bottom of turn five is not the time to see just what your guy is made of.
He might know exactly what the model is and still decide that it's not worth it in the end. I do it all the time. I may know that one particular Tyranid model is important, but after looking at how many claws it has and how long it's tail is... you know what, forget it, I'll just go around it and leave it alone.
The downside to standing out among the crowd.
They say the squeaky wheel gets the oil. If I look across the table and all of your models are two inches tall except for one single model that stands over 6 inches tall... I'd like to know just what that one does.
If you make your HQ larger than life, it can be hard to hide on the battlefield. If you're comfortable knowing that you can't really hide anywhere (except maybe inside a vehicle), then go with it.
Are you going to draw attention and lots of firepower? You most certainly are. If you're prepared for it though and you know that it's going to happen, then you can deal with it.
Sometimes you want to announce to the enemy where you're at. When you have the ability to deal with whatever comes your way when you do, it's not a problem. But what if you can't deal with all of it?
How modeling to blend in can be a benefit
This guy is the perfect example. The only thing that sets him apart from all the other models in the army is the Imperial icon on the top of his armour.
He's the only one in the whole force to have anything "Imperial" on him. It's enough to set him apart, but not too much.
Just like before, this doesn't change his stats, but can give an uncareful opponent a false sense of security. I've actually always wanted to do this with my Deathwing army. Have a Librarian dressed in no armour, but just some ceremonial robes. He'd be painted the part of course, but he'd be much smaller than all the Terminators around him.
Truth be told, those are the models I look out for the most. Find the smallest guy in the Imperial Guard Command squad and avoid him at all costs. He's the one that can demolish a tank with his pinky. Thanks, I'll skip fighting that guy for now.
If you come across an enemy model with no weapons at all in his hands, it should be a red flag. Maybe he can't do anything... and maybe he can do it all.
It's hard to be tough guy when you're small
There is a downside to modeling your HQ smaller or less obvious than usual. You can't really puff him up and make him look tough. Sure he blends in and you can use that to your advantage, but you won't be convincing anyone to stay away based on your looks alone.
Which way is better?
They both affect how your opponent views your HQ and army. I'd say go with the one you like more. If you like the idea of a regular, unassuming Commander, then go with it. If you like the power armoured model scaled up to a 60mm mini-diorama base, then go with that.
Just know that either route you chose, you'll get the associated effects. Maybe you'll end up drawing more firepower that warranted and dying in the first turn in 9 out of 10 games. And maybe you'll have to remind yourself that you did field a Commander after each game and try not to keep putting him back in the case mixed in with a Tactical Squad.
Part 3: Using your HQ on the table