The problem with trying to explain why the Church did what that website says the Church did is that the Church didn’t do what that website says the Church did.
Clear?
For instance, the Didache (c. 100 AD) – probably the first Christian catechism – discusses confessing sins in church. The Bible repeatedly mentions both confession and forgiveness of sins (James; the Gospels; various Pauline letters). The Gospels make clear that men being able to forgive sins – rather than God alone being able to forgive them – was a stumbling block to Jesus’ teaching. Yet Jesus made clear that the Apostles had the power to forgive sins (“Whose sins you forgive, are forgiven”), and the BIble teaches that the Apostles’ powers passed to their successors. So forgiveness of sins by priests has been around from the beginning.
That website says the Church first separated clergy from laity in the early second century. Apparently the author is unaware of the Old Testament, which separated the Levitical priesthood from the non-priests; the Gospels, which said that the priesthood was taken away from the Levites and given to others; and the New Testament letters, which discussed the rules for choosing bishops, priests, and deacons.
That website says that the Church first started having meetings of elders in a region in the second century. Trying reading Acts of the Apostles, which chronicles such meetings, or some of Paul’s letters (e.g., Timothy and Titus).
It says that clergy were prohibited to marry in the third century. That’s untrue in two ways. First, even today married men may become priests in the Catholic Church, just not in the Latin Rite (there are 13 other rites that allow it). Second, celibacy is celebrated in Paul’s letters – the very Bible that the site you cite claims to follow – as the ideal state.
As for Purgatory, since that’s one you specifically asked about, Jesus discussed it (the unforgiveable sin is one that cannot be forgiven, “neither in this age nor in the age to come”), so it’s Biblically based. Not to mention the fact that the Jews prayed for the dead
before the New Testament was written, so it can’t be a later invention by the Catholic Church.
It goes on and on, and it’s wrong. Why? Because, by attacking a
misrepresentation of the Catholic Church, it’s easier to justify staying in a different church.
Now, it is true that the theology explaining these doctrines has developed over time. Why? Because, as humans, we keep asking questions, and the answers therefore become more developed as the centuries pass by. Think about raising a child in a home with a fireplace. You begin by prohibiting the child from getting too close to the fire. At some point you start explaining that the fire is dangerous, and you soon answer “Because it would hurt you. Because it’s hot. Because fires are hot. Because etc…” Eventually you even have the child starting the fires once s/he’s old enough.
From the child’s perspective: are you inventing things as time goes on, or are you figuring out a more sophisticated explanation once you’ve understood the more simplistic ones?
In truth, however, the underlying rule was unchanged: Do not allow children to harm themselves through ignorance.
And that basic rule, like the doctrines you’re asking about, has been around from the beginning.