We're running the emulator CLI, using the latest API 30 AOSP ATD x86 image, on an x86_64 host, like this:

/android-emulator-sdk/emulator/emulator -avd emulator-avd -no-boot-anim -read-only -verbose -no-window -sysdir ./system/x86 -system ./system/x86/system.img -ramdisk ./system/x86/ramdisk.img -qemu -enable-kvm

On emulator 31.2.10:

INFO    | Android emulator version 31.2.10.0 (build_id 8420304) (CL:N/A)
INFO    | Found AVD name 'emulator-avd'
INFO    | Found AVD target architecture: x86
INFO    | argv[0]: '/android-emulator-sdk/emulator/emulator'; program directory: '/android-emulator-sdk/emulator'
INFO    | emuDirName: '/android-emulator-sdk/emulator'
INFO    | Probing for ./system/x86/kernel-ranchu-64: file exists
INFO    | try dir /android-emulator-sdk/emulator
INFO    | Trying emulator path '/android-emulator-sdk/emulator/qemu/linux-x86_64/qemu-system-x86_64'
INFO    | Found target-specific 64-bit emulator binary: /android-emulator-sdk/emulator/qemu/linux-x86_64/qemu-system-x86_64
...

and the emulator starts successfully.

On emulator 31.3.10:

INFO    | Android emulator version 31.3.10.0 (build_id 8807927) (CL:N/A)
INFO    | Found AVD name 'emulator-avd'
WARNING | Failed to process .ini file /home/coder/.android/./config.ini for reading.
WARNING | Found AVD target architecture: arm
INFO    | Found AVD target architecture: arm
INFO    | argv[0]: '/android-emulator-sdk/emulator/emulator'; program directory: '/android-emulator-sdk/emulator'
emulator: INFO: Use user provided system path ./system/x86
INFO    | emuDirName: '/android-emulator-sdk/emulator'
emulator: INFO: Use user provided system path ./system/x86
INFO    | Probing for ./system/x86/kernel-ranchu-64: file exists
INFO    | try dir /android-emulator-sdk/emulator
INFO    | Trying emulator path '/android-emulator-sdk/emulator/qemu/linux-x86_64/qemu-system-aarch64-headless'
INFO    | Found target-specific 64-bit emulator binary: /android-emulator-sdk/emulator/qemu/linux-x86_64/qemu-system-aarch64-headless

Eventually failing with this:

ERROR   | This AVD's configuration is missing a kernel file! Please ensure the file "kernel-ranchu" is in the same location as your system image.
ERROR   | ANDROID_SDK_ROOT is defined (/android-emulator-sdk) but cannot find kernel file in /android-emulator-sdk/system-images/ sub directories

(Note: we pass the -sysdir arg explicitly, since our system images are not stored in the SDK directory.)

Found AVD target architecture: arm, thus trying to run qemu-system-aarch64-headless, seems likely to be the root cause?