Learn English – ‘Natural body ____’ — “smell” vs. “odor” vs. “fragrance”

At least in regular, casual use, you're not going to find a real single-word equivalent for what you're looking for. However I'd like to address some of what you wrote:

First, "smells" on its own will only have one meaning, and that is a bad one. I cannot imagine a situation in which saying "it smells" would mean that something has a pleasant odor.

As mentioned in comments, "smells good" is actually the preferred or most common way to say it. It doesn't have to be the exact phrase "smell good," you can attach any adjective to it that you want. It just needs to be the adverb for "smell." You can twist it around and use it as an adjective, too. For example, you can have cake that smells delicious or you can have delicious-smelling cake. This phrase is more versatile than it seems, and you can use it with other words too, like taste. This is not to suggest that using other words are wrong, just that this is the "normal" way to say it.

Third, as for "rarely used loanwords," I'm not sure that the three you suggested there are really candidates for this description. Aromatic is commonly used, however if you were to say it I would think you were trying to sell me bath soap or something. Nevertheless it is used, and it can be used as the word that you are looking for, one that refers specifically to something that smells good, but ultimately "smells good" wins because it's used more. Delicious... rarely used? Are you talking about a "delicious odor" or something? Because delicious is a very common word as long as we're talking about food. Fragrant is also used fairly often, but it refers mostly to "things" and not to food. It's more about the property that something has intrinsically of smelling good. I also disagree that they refer to intensity of an odor. Aromatic and fragrant specifically refer to something that smells good.

So is there a better word? Honestly you can take your pick from just about any of the things you listed, but "smell good" is a perfectly fine two-word solution where you don't really need one word. You can twist it grammatically to be used like a single word, so you're not really limited, and you can change "smell good" to "smell delicious" or "smell wonderful" or anything you want.

Ultimately I think the more interesting question here is why from "taste" we get "tasty," which means "tastes good," but from "smell" we get "smelly," which means "smells bad."

The first question asks for a comparison:

What does it smell like?

Possible answers:

It smells like gingerbread.
It smells like fruity wine.
It smells like a cesspool.

The second question asks for a word describing the quality or goodness of the aroma:

How does it smell?

Possible answers:

It smells great!
It smells terrible.
It smells like a cesspool.

Okay, why did I use that last one for both questions? Because everyone knows a cesspool smells awful, so it works for the second question. It's essentially the equivalent of:

It smells awful – like a cesspool.