Anglophones often use our relatively small set of verb tenses/moods/etc. quite loosely (we've only really got "past" and "not-past", modified by various modal/auxiliary verbs). So it's simply too broad a subject for me to cover all "past" tense, "did/didn't happen" usages here.
But OP's context specifically concerns the difference between referencing a past situation that might or might not have happened (at time of speaking it's unknown), as opposed to a "hypothetical irrealis past" (which in principle could have happened, but the speaker knows that actually it didn't).
1: "If he has taken the plane he will be here soon" (speaker doesn't know what travel mode he used)
2: "If he had taken the plane he would be here soon" (speaker knows he didn't take the plane)
It's quite possible to use simple past "If he took the train..." in both those examples. In the case of...
1a: "If he took the plane he will be here soon"
...it's just a simpler alternative to #1 above, which I think would always have exactly the same meaning. Arguably the more complex verb form in #1 makes that meaning more "instantly accessible" to the audience - but both forms are perfectly valid, and are in common use,
But when we consider...
2a: "If he took the plane he would be here soon"
...it's no longer a fixed part of the meaning that he didn't take the plane. The speaker could say this to his wife while she's on the phone to their son, discussing whether the parents are willing to pay for their son to take a plane rather than a train (i.e. - even the decision about which travel mode to use hasn't yet been taken, so we're obviously not talking about a "past" event).