Philz has an option to use the newer updater script or an older legacy script. If your rom has an older update binary, it uses that script to flash your file. Newer update binaries run on the new script and don't need that step.
Basically, it's a work around to make any file flashable, because not every file out there has an updated update binary to work on the newer recovery versions. Philz is the only recovery with that kind of a workaround, cwm would simply throw an error and won't flash the file.
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No
New version detects that and there is no more issues. Get latest binary from a CM11 nightly