Learn English – Is “believe you me” proper English

There is actually a subtle distinction between the two words: undoubtedly means "not doubted" whereas indubitably means "beyond doubt" i.e. that which cannot be doubted as opposed that which is not doubted.

This answer serves to illustrate, in part, the more general question you've raised. There is a phenomenal plethora of synonyms in English (Hungarian takes the trophy, though) and it is largely due to the language's mongrel heritage, in turn caused by successive waves of conquerors and invaders putting down roots in the land. We have roots in a number of Celtic, West Germanic and Romance languages, and so an extraordinary arsenal of vocabulary has been available to us. As a result, we have been able to use these synonyms to inject the language with subtler shades of meaning than would be afforded by a single linguistic root. Why this quality is more apparent in English than in some other languages is not entirely clear (we're certainly not unique in our mongrel heritage) and the debate continues among linguists today.

Regarding "pretentious" synonyms, I believe this has its origins in the days when French was the language of the court and Latin that of the clergy, while common old guttural, germanic, dialectic English was the language of the peasantry. The association of Romance languages (and therefore longer words of latin-style inflection) with the higher classes of society has stuck with us, and the hangover of this can be observed, for example, in the extensive use of French in "legalese."

Here is a hypothetical conversation where emphasis on did might make sense:

Speaker A: "You look sweaty. Were you working out at the gym?"

Speaker B: "No, I didn't come from the gym."

Speaker A: "Well, where did you come from?"

Speaker A wants to elicit an affirmative statement by that emphasis. The emphasis also expresses annoyance at Speaker B's uninformative negated response.