The geom_eli module lacks version information. When a kernel has the geom_eli module compiled in, but bsdinstall told the loader to load the module via loader.conf (for example, full-disk encrypted setups), the kernel will reload the module later on in the boot process, causing geli to wipe the cached passphrase and prompt the user a second time for it. Setting the module version should tell the kernel to only load it once.
Looks like that commit was made after this patch was posted for review. Given that it now includes MODULE_VERSION (but without using G_ELI_VERSION), we can probably just keep with what was committed. Should I close this review?