It seems unlikely that they are making more profit per licensed set because they are likely having to pay a cut to a third party (for example, Disney gets a cut of each Star Wars set sold).

So if their license free sets sell better, then it would stand to reason they make more profit off of these.

And a licensed set often has to amortize the cost of tooling made specifically for it.

LEGO is very good at recycling shapes in different colors as special parts for sets. The biggest tooling costs are in the minifigs for special sets, those are almost always there because custom minifigs are an easy way to make a set unique. That way you drive sales because people can't make the set from loose parts.

Those are royalty free.

It should be easy to determine if they are more profitable assuming some kind of percentage going to the brands. If the mark-up is lower than a small percentage they are likely not more profitable, otherwise likely they are more profitable on a unit basis (per set).

Profits are certainly higher with Friends and City than with Star Wars. Lego saves a lot on licensing there. And the Star Wars sets are a bit more pricey, but per piece the difference isn't that big.