It sounds to me like RAM and SSD are your biggest limiting factors here, since the CPU and GPU are not being utilized that hard.

So if I were you I would buy a lot of memory and the fastest SSDs possible. I admittedly do not know anything about the software you are using, but you might want to reach out to the community that uses the software and ask if having the data stored on a separate drive from the operating system will help with preventing the drive from getting overloaded.

Realistically either Intel or AMD will give you the ability to use a lot of RAM and a fast PCIe 4.0 drive, but in a technical sense the latest Intel Alder Lake CPUs when installed on an H670 or Z690 board will give you the maximum amount of possible throughput for the SSDs, which might matter to you if you want this system to keep up with future iterations of this software (but I'm just guessing here).

The latest Intel CPUs do not actually run that hot, outside of the 12900K which can run very hot when pushed to 100% load. But it doesn't seem to me like you actually need such a CPU.

If I were you I'd probably consider something like a 12400 or 12700 on an H670 board. But definitely ask within the software's community as well.

(BTW my dad works in hydrogeology but I don't believe he uses Modflow, now I'm curious tho)