La komercisto redonas ŝanĝmonon, malgraŭ tio, ke moneroj mankas.

Because ŝanĝmono is the direct object of redonas.

The merchant gives back what?
→ ŝanĝmonon

In Esperanto, direct objects normally take the accusative ending -n.

• La komercisto redonas ŝanĝmonon. = The merchant gives back change.
• La komercisto redonas monon. = The merchant gives back money.

Redoni means to give back or to return. It is built from:

• doni = to give
• re- = again / back

So redonas literally means gives back.

That fits the idea of change very well: the customer gives money to the merchant, and the merchant gives part of it back as change. Using donas would not be impossible in some contexts, but redonas is more precise here.

Yes. Ŝanĝmono is a compound noun, and Esperanto uses compounds very often.

It is made from:

• ŝanĝ- = change / exchange
• mono = money

So ŝanĝmono means change money, i.e. change.

This is very normal Esperanto word-building. English often uses separate words where Esperanto prefers a compound.

It means despite the fact that or although.

Here:

• malgraŭ = despite
• tio = that / that fact
• ke = that

So malgraŭ tio, ke moneroj mankas means despite the fact that coins are lacking.

A very natural shorter alternative would be:

• La komercisto redonas ŝanĝmonon, kvankam moneroj mankas.

Here kvankam also means although.

Because malgraŭ is primarily a preposition, and prepositions normally go before a noun phrase, not directly before a full clause.

So:

• malgraŭ la pluvo = despite the rain
• malgraŭ la problemoj = despite the problems

But when what follows is a whole clause, Esperanto often uses tio, ke as a bridge:

• malgraŭ tio, ke moneroj mankas

Literally, this is something like despite that, that coins are lacking, but in natural English it just means although coins are lacking.

There are two punctuation points here for clarity.

First, the comma before malgraŭ separates the main clause from the following concessive clause:

• La komercisto redonas ŝanĝmonon, ...

Second, the comma after tio is part of the common pattern tio, ke.

Esperanto punctuation is generally quite clear and practical, and commas often mark clause boundaries more explicitly than in English.

Because manki works differently from the English verb to lack.

In Esperanto, manki usually means to be lacking or to be missing, and the thing that is missing is the subject, not a direct object.

So:

• Moneroj mankas. = Coins are lacking. / Coins are missing.

Not:

• monerojn mankas

That would be wrong, because manki does not take a direct object here.

A very useful pattern is:

• Al mi mankas mono. = I lack money.
  Literally: Money is lacking to me.

So if you want to say who lacks the coins, you could say:

• Al la komercisto mankas moneroj. = The merchant lacks coins.

They are related, but they are not the same thing.

• ŝanĝmono = change, the money returned after payment
• moneroj = coins

So the sentence is not repeating itself. It says the merchant gives change back, even though coins are lacking.

That suggests the merchant may still manage to give the correct change somehow, even if there are not enough coins available.

Because Esperanto does not use the definite article unless the noun is specifically definite.

Here:

• ŝanĝmonon means change in a general or context-based sense
• moneroj means coins in general, not a specific previously identified set of coins

Also, ŝanĝmono behaves like a mass noun, similar to money in English, so it often appears without la.

If you used la, it would sound more like you mean a specific, already identified thing:

• la moneroj = the coins
• la ŝanĝmono = the specific change already being referred to

Yes. In this sentence, kvankam would be a very natural alternative.

So you could say:

• La komercisto redonas ŝanĝmonon, kvankam moneroj mankas.

That means essentially the same thing.

A helpful way to think about it is:

• malgraŭ + noun phrase
• malgraŭ tio, ke + clause
• kvankam + clause

All of these are common, but kvankam is often the simplest choice before a full clause.