However, as a result, the difference between an Opus decode and the original will only get you lossless reconstruction if you decode with the same build of Opus on the same machine. Also, since Opus uses IIR filters that ring to infinity, even on the same machine you only get bit-exact results if you decode each file from the beginning. It won't work if you seek.
Really, if you're concerned about the disk space required for separate FLAC and Opus encodes, delete the Opus version. FLAC decoding is extremely fast (5x faster than Wavpack), and Opus encoding is pretty efficient, too (on the same order as Wavpack decoding).