Is there a logical rationale for grouping people by state for federal government representation today (e.g. the US Senate)? I understand that precedent and reluctance to fundamentally alter the US constitution are perhaps reason enough for most, but barring these arguments, if the bicameral legislature were to be redefined today, what arguments would be used on the side of state-based seat allocation for the Senate? For argument purposes consider a proportional representation scheme such as open party-list proportional representation as an alternative.
I think this question devolves into the question of "What are the modern benefits of states?".
The Senate was originally designed to represent state governments the way that the House was designed to represent the people in each state. This was later changed by the Seventeenth Amendment to allow the direct election of Senators, but they still represent the entirety of their state, the way they did when the government picked them. As long as each state has its own government which needs to address all the disparate concerns of its citizens (both urban and rural), then it makes sense to have representation at the national level of that same unit of population.
Additionally, the current Rural/Urban divide in politics is a relatively new situation. Compare the county-by-county maps from 1920 (100 years ago), 1968 (52 years ago), 2000 (20 years ago) and 2020 (now) - you can see that what used to be regional groupings by party has been gradually diffusing across the country. But that doesn't mean that this division is permanent. 20 years from now, it's very possible that the varying effects of climate change being the most important dividing issue, and the eastern states are opposed to the western states in how to best handle it.