Learn Spanish (Latin America): Pon el explosivo en la caja, como he dicho. - Put the explosive in the box, as I have said.

Because this specific clause isn't a threat! Here, como simply means "as" or "in the way that" based on a stated fact, so it takes the indicative. It only triggers the subjunctive when used as a conditional warning, like Como dejes caer el explosivo, explotará (If you drop the explosive, it will blow up).

Pon is the affirmative command. Just as a quick refresher, how would I make this negative ("Don't put")?

You would use the present subjunctive: No pongas el explosivo. The short, irregular form pon is strictly for affirmative tú commands.

The sentence uses the present perfect (he dicho). Would Latin American speakers use the simple past (dije) here instead?

Yes, very often! While he dicho is perfectly understood, many Latin American regions strongly prefer the preterite for actions that feel completely finished. Saying como dije (as I said) is incredibly common and sounds very natural here.

Could I use tal como instead of just como in this sentence?

Yes, you can say tal como he dicho. Adding tal adds emphasis, meaning "exactly as I have said" or "just as I have said." Given the serious context of handling an explosive, that extra strictness fits perfectly!