My impression is that the difficulties you encounter never occur to me, but I am a Windows user.
For example, I can simply go to File > Save Config in the waveform viewer, and the new plot setup is saved for the next simulation to run and load (with no config read-only issues).
I also haven’t encountered a bug where a slight mouse movement causes the plot config to reload. How large is your .qraw file? My impression is that weird issues may occur if the .qraw file is larger than several gigabytes. QSpice defaults to saving data for every node, including subcircuits. If you are running a very complex schematic, you might consider limiting what to save with the .save command, or controlling how frequently data is written using the .option culltime command.
Qspice : Not Responding - QSPICE - Qorvo Tech Forum
Hesham Omran developed a waveform viewer for Ngspice, LTspice, and QSpice. I have never used it, but you might want to give it a try since it supports Linux. Here is the information for your reference:
https://github.com/omranh/spice-station-ai-releases
https://www.linkedin.com/posts/omranh_spice-analog-vlsi-activity-7464661220403609600-Rovi/