Ili faras interkonsenton, malgraŭ tio, ke la prezetikedo mankas.

Because it is the direct object of faras.

• Ili faras = They make / do
• interkonsento = agreement
• interkonsenton = agreement as the thing being made

Esperanto uses -n to mark the direct object, so faras interkonsenton literally means make an agreement.

Yes, and that is normal. Esperanto often uses very straightforward verb+noun combinations.

• fari interkonsenton = to make an agreement
• In natural English, you might say make an agreement, reach an agreement, or come to an agreement

So the Esperanto phrase is completely normal even if English might prefer a slightly different expression in some contexts.

It means despite the fact that or although.

You can break it down like this:

• malgraŭ = despite / in spite of
• tio = that / that fact
• ke = that

So:

• malgraŭ tio, ke la prezetikedo mankas
  = despite the fact that the price tag is missing

This is a common Esperanto structure when a whole clause follows malgraŭ.

In standard Esperanto, malgraŭ is normally followed by a noun phrase, not directly by a clause.

So Esperanto prefers:

• malgraŭ tio, ke... = despite the fact that...

Here tio acts as the thing that malgraŭ governs, and the ke clause explains what that tio is.

This is similar to English despite the fact that...

Manki means to be missing / to be lacking / to be absent.

In this sentence:

• la prezetikedo mankas = the price tag is missing

Here, la prezetikedo is the subject, not an object. The idea is not someone lacks the price tag, but rather the price tag is absent.

So manki often works differently from English verbs like lack.

Compare:

• La libro mankas. = The book is missing.
• Al mi mankas tempo. = I lack time / I am short of time.

In the second type, what is lacking is still the subject:

• tempo mankas = time is lacking
• al mi = to me

Yes, and in this sentence is missing is the most natural translation.

• la prezetikedo mankas = the price tag is missing

That is usually better English than the price tag lacks, which would mean something different.

So when you see manki, do not always translate it mechanically. Its natural English equivalent depends on the context.

It is a compound word:

• prezo = price
• etikedo = label / tag

Together:

• prez-etikedo = price tag / price label

Esperanto commonly forms compounds this way. The last part is usually the main idea, and the earlier part modifies it.

So prezetikedo is a kind of etikedo, specifically one connected with price.

Because the speaker has a specific price tag in mind: the price tag.

In context, this probably refers to the tag on a particular item already being discussed. Esperanto uses la much like English the for something specific or identifiable.

So:

• prezetikedo = a price tag / price tag
• la prezetikedo = the price tag

Because Esperanto uses the present tense -as for present actions or states.

• faras = do / make / are making
• mankas = is missing / is absent

Depending on context, English may translate this as simple present or present progressive, but Esperanto just uses -as.

So:

• Ili faras interkonsenton could mean They make an agreement or They are making an agreement
• la prezetikedo mankas = the price tag is missing

Yes, a sentence with kvankam would also be possible.

• Kvankam la prezetikedo mankas, ili faras interkonsenton. = Although the price tag is missing, they make an agreement.

The difference is mainly one of phrasing:

• malgraŭ tio, ke... = despite the fact that...
• kvankam... = although...

Both are correct, but malgraŭ tio, ke feels a bit more literally like in spite of that fact.

Ke introduces a subordinate clause, usually corresponding to English that.

In this sentence:

• malgraŭ tio, ke la prezetikedo mankas

the part after ke is the clause:

• la prezetikedo mankas = the price tag is missing

So ke links that fact (tio) with the explanation of what that fact is.

Yes, the commas help separate the inserted subordinate phrase:

• Ili faras interkonsenton, malgraŭ tio, ke la prezetikedo mankas.

The phrase malgraŭ tio, ke la prezetikedo mankas is a parenthetical or adverbial part explaining the circumstance. Esperanto punctuation is often fairly logical and helps show structure.

You may also see similar comma use around subordinate clauses in other sentences.