Learn Finnish: Hänet oli haudattu yksin, vaikka hauta oli iso. - He had been buried alone, although the grave was big.

You are right that passive objects usually take the nominative form. However, personal pronouns (like hän) are a major exception. When a personal pronoun is the object of a passive verb, it always takes its special accusative form ending in -t, making it hänet here.

How exactly is the pluperfect passive formed in oli haudattu?

It is formed using the active 3rd person singular past tense verb oli (was/had) plus the passive past participle of the main verb, which here is haudattu (buried). Notice that the auxiliary verb is the active oli, not the passive oltiin.

I sometimes hear people say oltiin haudattu. Is that the same thing?

In standard Finnish, oltiin haudattu is not used for the passive. However, in spoken Finnish, the passive form is commonly used to mean 'we'. So in everyday speech, me oltiin haudattu means 'we had buried', while the standard Finnish oli haudattu used in this sentence translates to 'had been buried'.

Is the verb haudattu related to the noun hauta used later in the sentence?