Alas, it's not possible for the moment.
flvtool2 works by loading the input file in its entirety in memory,
which can lead to a big memory consumption.
FLVmeta, on the contrary, reads the file one first time to gather
statistics in order to compute the new metadata, and then performs a
second reading to fully copy the file to the destination.
This requires the ability for the input stream to be seekable (by
going back to the beginning of the file), and unfortunately, stdin
lacks this ability.
One way to handle this would be to read stdin into a temporary file,
and work on this file instead, but a script could pretty well handle
that step around the invocation of flvmeta.
Regards,
Marc