The current kernel recipes in the meta-intel layer use the following convention
for kernel modules that need to be autoloaded:
KERNEL_MODULE_AUTOLOAD_core2-32-intel-common += "uio"

When using the override with the += operator we're only appending to the
override variable (KERNEL_MODULE_AUTOLOAD_core2-32-intel-common). Bitbake will
thus eventually substitue KERNEL_MODULE_AUTOLOAD by whatever
KERNEL_MODULE_AUTOLOAD_core2-32-intel-common contains, if core2-32-intel-common
is found in the OVERRIDES variable, effectively overriding all previous content
of the variable KERNEL_MODULE_AUTOLOAD that other layers may have modified.

Unless this is intended, the preferred way to add a kernel module to the
autoload list would probably be the following:
KERNEL_MODULE_AUTOLOAD_append_core2-32-intel-common = " uio"

This will append to the KERNEL_MODULE_AUTOLOAD variable in case
core2-32-intel-common is found in the OVERRIDES variable (i.e. it will not
override the variable as it happened in the previous case).

Steps to reproduce the issue:
clone poky, meta-intel and meta-virtualization from git.yoctoproject.org
clone meta-openembedded from git.openembedded.org
Make sure the following layers are added in conf/bblayers.conf:
  meta-intel
  meta-openembedded/meta-networking
  meta-virtualization
In conf/local.conf make sure MACHINE is set properly, and add some kernel
modules to the image:
MACHINE = "intel-corei7-64"
IMAGE_INSTALL_append = " kernel-module-kvm kernel-module-kvm-intel kernel-module-uio"

Now build core-image-minimal:
bitbake core-image-minimal

In the final image, check the contents of /etc/modules-load.d/. Although
meta-virtualization adds kvm and kvm-intel to KERNEL_MODULE_AUTOLOAD, the
directory only contains the "uio" module. This is because all other modules
have been overriden by the kernel recipes in meta-intel.