You mean transcode the VC-1 file again, correct?
If that is the case then the H.264 file could be even higher quality, it depends on the bit rate and settings chosen. There is an amazingly wide range of possible qualities using H.264 or H.265, depending on the settings chosen.
H.265 is obviously better quality when the bitrate is a bit lower than what H.264 looks very good at, but at bitrates where H.264 looks very good it often looks better than H.265 (it keeps a little more detail and sharpness). The difference is relatively subtle now, assuming you chose your x265 options well (e.g. --no-strong-intra-smoothing is important at higher bitrates), but H.264 is still a very high quality option.
I strongly recommend
Handbrake instead of CloneBD.