Is there a way to refresh the current configuration used by modprobe with a newly updated modules.conf file?

If you're just testing modules out, you should be able to use modprobe <module> and modprobe -r <module> to insert and remove modules from the linux kernel, respectively. insmod and rmmod should also perform the same functions (inserting and removing).

EDIT:

It sounds like you're looking for the mapping directive in /etc/networking/interfaces. See man interfaces for details on how to alias networking devices. Note that terminology-wise, an "alias" is a second, third, or otherwise additional IP for an IP device, resulting in an interface with multiple IPs. A "mapping" is used to map logical interface names (ifconfig LOGICAL_INTERFACE up) to real interface names.

Old question but I think it can help someone who find an answer. In systemd modules loads with service systemd-modules-load. You can check status with command:

sudo systemctl status systemd-modules-load.service

or reload modules with command:

sudo systemctl restart systemd-modules-load.service