Questions about "why a law is ..." are political questions not legal questions and you may get better traction on politics. However, I will address the legal issues and offer some speculation on the politics.
The states named in the preamble to the Constitution (an Act of British Parliament) as original states were New South Wales, Victoria, Queensland, South Australia and Tasmania. Western Australia was not named at the time of the passing of the Act or Royal Assent because the people of that colony had not vet made their mind up.
WA decided to join in a vote held on 31 December 1900 and Australia came into being on 1 January 1901. Therefore, even though not named as such, WA was an "original state". Since all 6 states in the Federation are "original states" the clauses have no practical effect at present.
However, there have been a number of proposals to add new states, either by subdividing existing states or by granting statehood to the territories of Northern Territory and/or the Australian Capital Territory. If such were to come to pass, the clauses would have practical effect.
In 1998, Norther Territorials rejected an offer of statehood that would have given them 3 senators as a state and 2 representatives based on population (currently they have 2 senators and 2 representatives). Clearly, they were not being given the same privileges as an "original state".
In 2015 all Australian governments agreed in principle that the NT should become a state by 2018, however, as it is now 2017 and no action has been taken this seems unlikely.
Politics is complicated: just as much in the late 19th century as it is in the early 21st. Negotiations between the colonies were fraught and federation was by no means a certain outcome. New Zealand and Fiji dropped out early and each forged its own path to nationhood. However, by the late 1890s it was clear that the 5 eastern colonies would federate with or without Western Australia.
It seems likely that this provision served multiple purposes including:
- putting pressure on WA to join at the outset - the deal they got as a "Johnny come lately" may not have been as good.
- protecting "white" Australia - the drafters of the Constitution were men of their times, that is to say: racist, misogynist bigots. Any non-original states were likely to be former British colonies in the Pacific or South-East Asia, this clause would allow the nation to reduce the influence these non-white states might have.