Learn Dutch: Dat klopt inderdaad. - That is indeed correct.

The rule you are learning applies when dat is a connecting word between two clauses (a subordinating conjunction, like in "I know that he is here"). In this sentence, Dat is simply a demonstrative pronoun meaning "That", and it acts as the subject. Because this is just a normal main clause, the verb klopt stays in the standard second position.

Doesn't the verb kloppen mean "to knock"?

Yes, literally kloppen means "to knock" (on a door) or "to beat" (like a heart). However, it is very commonly used as an expression meaning "to be correct" or "to add up". Saying Dat klopt is the standard, most natural way a Dutch person will say "That's right" or "That is correct."

Could I just translate the English literally and say Dat is inderdaad correct?

You could, and it is grammatically correct. However, in everyday conversation, native Dutch speakers almost always prefer the verb kloppen over using the adjective correct.

If I wanted to emphasize the word "indeed", could I put inderdaad at the beginning of the sentence?

Yes, but remember your "verb-second" rule! If you move Inderdaad to the first position, the verb must stay in the second position, forcing the subject (dat) to move behind it. The sentence would become: Inderdaad klopt dat.