Well to take the most obvious problem, each California congressional district has to have roughly 750k people but Los Angeles County has 9.9 million.

I get that, and yet the root of my observation is simply that there are are already existing valid political boundaries. The core problem with legislative and congressional districts is that they are utterly arbitrary and subject to change based on political whims (yes I understand there is also a nominal census reasoning as well). My point then is simply: could there be permanent, non-arbitrary boundaries that would no longer be subject to political manipulation?

I don’t think so! Even permanent and supposedly non-arbitrary boundaries are subject to intense political contestation. Observe how in the first decades of this country’s history states were often admitted in pairs, one slave and one free (for instance Missouri and Maine), in order to maintain the balance of power.