Learn French: Le développeur a failli formater l'ordinateur. - The developer almost formatted the computer.

While a presque formaté is understandable, using faillir in the passé composé followed by an infinitive is the most natural and idiomatic way in French to say you came very close to doing something. It strongly emphasizes the 'near miss' aspect—an action that was on the verge of happening but ultimately did not.

Could we use faillir in the present tense here to mean 'he almost formats'?

No, when meaning 'to almost do something,' faillir is almost exclusively used in the passé composé. In modern French, if you use faillir in the present tense, it usually means 'to fail' or 'to default on' something, not 'to almost do' it.

If I want to replace l'ordinateur with a pronoun to say 'The developer almost formatted it,' where does the pronoun go?

The pronoun goes directly before the infinitive, not before the auxiliary verb. You would say: Le développeur a failli le formater. This is the standard rule for object pronouns when dealing with a semi-auxiliary verb followed by an infinitive.

Does faillir always imply a near miss of something bad, like accidentally erasing a computer?

It frequently does, because it comes from the same root as 'failing' or 'fault.' It is heavily used for narrow escapes or mistakes, like J'ai failli tomber (I almost fell). However, you can occasionally use it for positive or neutral things too, where it still carries that sense of a sudden, narrow margin.