There still isn’t a way to specifically pick a version to download. However, if you set your download quality to better match the version you want, it should trigger PMS to download that version instead of transcoding a higher version.
i.e. if your 1080p is 20 Mbps and the 720p is 10 Mbps, setting the download to 12 Mbps should end up downloading the 720p version.
You can test this by first setting the regular quality setting and playing a file. If the version you want plays as direct play, then the Download should work with the same Download quality setting.