I think you and OP are talking past each other. A purely proportional voting system is not a good idea for the reasons you mentioned. That's why a lot of countries including the US have a bicameral system: One where regions/states are represented proportionally and one where seats are distributed equally.

I believe OPs critic is wrt the district based voting system of the House of Representatives. Having a winner takes it all system per district seat is a really bad idea and just a result of a limited understanding of election dynamics at that time and some restrictions how election results could be communicated before the advent of telegraphy:

A proportional system forces states to first collect all votes from all districts (a huge task for a state like Texas when only horses and a few rail roads are available for transportation) then collecting and counting the votes at the capital of the state and then sending messengers back to each district to announce results. When each district calculates their winner independently this problem is alleviated.

Nowadays it's clear that such a system will inevitably create a two party system. The fact that the president is also elected by an electoral college (which in most states is also a winner takes it all system) further enforces an effective two party system.