At their core, en anka is a domesticated duck while en and is a "wild" duck.
Anka might sometimes be used in a more wide sense - rubber/plastic ducks are called gummiankor or plastankor for example. And the inhabitants of Duckburg are ankor, despite not being domesticated so much as civilized.
That's an interesting question. Although I did some toponymy research for a university essay a year ago, I'm afraid I'm not an expert per se on the suject. But as a native, I can say that Ankeborg is much more how a Swedish city name would behave linguistically. Nonetheless I'll give you my five eurocents:
My theory is that this has to do with a feature that's a bit beyond being taught on the farly fundamental (but thorough!) level that is the case on Duolingo. This feature has to do with how words behave when they form compounds. Generally, when a compound is formed out of three words and the second ens in a consonant, a little S will appear between the second and third word. There are lots of exceptions and tricky things about this rule, and words that will take the -S even in compounds of two words. Furthermore, in some words this little letter can change the meaning. Landsvägen is the country road, but landvägen is the overland route as opposed to a sea route.
Then we have the vowels in vowel-final words. Many words, predominantly those that were of use already in medieval Swedish or before, will change or remove or add a vowel in a compound. Thus we have kyrka, hälsa, gata, kung, anka (church, health, street, king, duck) but kyrkogård, hälsosam, gatukök, kungadöme ankbröst (graveyard, healthy, street food stand, kingdom and duck breast). To make this even worse, gata will in some compounds form gatu- and in some others just gat- (gatsten "sett paving")
Historically, these forms are genitive forms of the nouns. Medieval Swedish (and old Norse) required the first word in a compound to be in the genitive. These forms have been 'frozen' in time when Swedish developed and the case system was lost, in that they remain in the way we use words to form these compounds. However, they carry no grammatical meaning, being just the idiomatic ways of speaking Swedish.
Perhaps this text could use a little better disposition, but hopefully you'll get the hang of it.