[Nexus 5 Android Development] Case_:
I am using this ROM as a secondary on MultiROM. You have to delete a few lines from updater-script in the ZIP file for it to work, but it works just fine (for me, anyways, YMMV).

Basically, just change the updater-script in downloaded ZIP at /META-INF/com/google/android/ with something like this:

assert(getprop("ro.product.device") == "hammerhead" || getprop("ro.build.product") == "hammerhead" || abort("This package is for device: hammerhead; this device is " + getprop("ro.product.device") + "."););
mount("ext4", "EMMC", "/dev/block/platform/msm_sdcc.1/by-name/system", "/system", "");
package_extract_file("system/bin/backuptool.sh", "/tmp/backuptool.sh");
package_extract_file("system/bin/backuptool.functions", "/tmp/backuptool.functions");
set_metadata("/tmp/backuptool.sh", "uid", 0, "gid", 0, "mode", 0755);
set_metadata("/tmp/backuptool.functions", "uid", 0, "gid", 0, "mode", 0644);
run_program("/tmp/backuptool.sh", "backup");
unmount("/system");
mount("ext4", "EMMC", "/dev/block/platform/msm_sdcc.1/by-name/userdata", "/data", "");
package_extract_file("system/bin/otasigcheck.sh", "/tmp/otasigcheck.sh");
package_extract_file("META-INF/org/cyanogenmod/releasekey", "/tmp/releasekey");
set_metadata("/tmp/otasigcheck.sh", "uid", 0, "gid", 0, "mode", 0755);
run_program("/tmp/otasigcheck.sh") != "31744" || abort("Can't install this package on top of incompatible data. Please try another package or run a factory reset");
unmount("/data");
show_progress(0.750000, 0);
block_image_update("/dev/block/platform/msm_sdcc.1/by-name/system", package_extract_file("system.transfer.list"), "system.new.dat", "system.patch.dat");
mount("ext4", "EMMC", "/dev/block/platform/msm_sdcc.1/by-name/system", "/system", "");
delete("/system/bin/otasigcheck.sh");
unmount("/system");
show_progress(0.020000, 10);
mount("ext4", "EMMC", "/dev/block/platform/msm_sdcc.1/by-name/system", "/system", "");
package_extract_file("system/bin/backuptool.sh", "/tmp/backuptool.sh");
package_extract_file("system/bin/backuptool.functions", "/tmp/backuptool.functions");
set_metadata("/tmp/backuptool.sh", "uid", 0, "gid", 0, "mode", 0755);
set_metadata("/tmp/backuptool.functions", "uid", 0, "gid", 0, "mode", 0644);
run_program("/tmp/backuptool.sh", "restore");
delete("/system/bin/backuptool.sh");
delete("/system/bin/backuptool.functions");
unmount("/system");
show_progress(0.050000, 5);
package_extract_file("boot.img", "/dev/block/platform/msm_sdcc.1/by-name/boot");
show_progress(0.200000, 10);

Remember that this one is based on the file from the current 12-02 ROM, another ROM (older or newer) might be using a slightly different updater-script, so you may need to adapt it a bit. But it should be pretty easy to modify any updater-script for anyone with a basic understanding of scripting if you compare this edited one with the original one - you just pretty much remove any parts where the updater-script tests if the necessary partitions are mounted (it seems that with current MultiROM, the tests are not only not needed, but for some reason cause problems).

And replace the original updater-script in ZIP at META-INF/com/google/android/ with the new one. The ROM should now flash as secondary without any problems. Been using this method for over a week with every nightly available here just fine.

But bear in mind that I'm not responsible for any problems this may cause you and tampering with updater-script file can be potentially dangerous. So try at your own risk. It works for me just fine, but that doesn't mean it will work for you as well.

Edit: Alternatively, if you don't want to copy and paste, I've attached the script above in this post as well. Just don't forget to remove the .txt extension - updater-script should have no extensions.