[Nexus 7 (2013) Android Development] tungdil:
If you don't mind risking to brick your device and are OK with some editing you could go as referenced in this MultiROM thread and explained in detail here. At least this works for me with cm-12-20141212-UNOFFICIAL-flo.zip

Unpack the updater-script from the zipfile (I like to do it in a separate directory, here named "cm12", but this is not absolutely required.)

mkdir cm12
cd cm12
unzip ../cm-12-20141212-UNOFFICIAL-flo.zip META-INF/com/google/android/updater-script

Edit META-INF/com/google/android/updater-script and remove the lines marked in red below:

assert(getprop("ro.product.device") == "flo" || getprop("ro.build.product") == "flo" || abort("This package is for device: flo; this device is " + getprop("ro.product.device") + "."););
[COLOR="Red"]ifelse(is_mounted("/system"), unmount("/system"));
[/COLOR]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");
[COLOR="Red"]if is_mounted("/data") then
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");
else
[/COLOR]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");
[COLOR="red"]endif;[/COLOR]
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);

Update the zipfile :

zip -u ../cm-12-20141212-UNOFFICIAL-flo.zip META-INF/com/google/android/updater-script

You'll likely see the following warning message which doesn't do any harm, as far as I can say:

updating: META-INF/com/google/android/updater-script
zip warning: Local Entry CRC does not match CD: META-INF/com/google/android/updater-script

Then flash the zip as usual in MultiROM.

Disclaimer: As you may have expected ;) No warranty that this works for you and, of course, you do everything at your own risk!

Credits go to [MENTION=1955641]Case_[/MENTION] for his post and [MENTION=4850572]thereal_bigjake[/MENTION] for pointing it out in the MultiROM thread.

Good luck!