The Privium system at Amsterdam airport does not require you to insert your passport in the machine or to show it to anybody. You do need a special Privium card, which contains the biometrics data, and are still supposed to have your passport with you, obviously. Enrolment in this system is voluntary (and starts at €121 per year). The regular automated passport control at Schiphol works differently and do rely on the passport's optical machine readable zone.
There are advantages to the use of passports for automated border checks: You don't need to install and secure widespread access to a sensitive database and you can support passports from other countries (for which you don't have access to any central database). In fact, you don't need any central biometrics database at all, which has clear security and privacy benefits.
Generally speaking, note that matching a person to a known set of biometrics (whether you read them from a chip or look them up in a database based on name and date of birth or a special identification badge) is a completely different problem than a wide search through a large biometrics database. The latter is significantly slower and brings up many false positives with the data available now (picture of the face and fingerprints). It can be used for investigation purposes, for things like asylum applications and in a few other contexts but it would not be practical for automated border checks.
Importantly, not all countries retain the data that's on the passport. And when they do, they do not always keep all the data, what they keep might not be centralised, or it might not be available for automated processing. Apart from India, it seems that no country systematically collects iris data either. Considering all this, it seems that your question is based on a rather optimistic (or pessimistic, depending on how you feel about all this) view of the state of biometric data collection and processing.