Learn Russian: Этот сейф пустой, но я намеренно запирал его утром. - This safe is empty, but I intentionally locked it in the morning.

This is a classic example of the 'annulled result'. The speaker locked the safe, but it is now empty (and thus must have been opened again). Because the result of the locking (the safe being closed and secure) is no longer in effect, Russian uses the imperfective запирал to show the action happened but its result was reversed.

What would the sentence mean if I used the perfective запер instead?

If you said я запер его, it would imply that the safe is still locked right now. That would sound strange next to the discovery that it is empty, since a safe usually needs to be open to check its contents. The perfective aspect emphasizes a result that lasts into the present.

Since сейф is an inanimate masculine noun, why is the pronoun for 'it' его? Doesn't the accusative form usually stay the same as the nominative for inanimates?

That animacy rule applies to nouns and adjectives, but not to personal pronouns. The pronoun он (which stands in for the masculine noun сейф) always becomes его in the accusative case, regardless of whether it refers to a living person or an inanimate object.

Could I use специально instead of намеренно here?