Minion doesn't touch SavedVariables since its in a different folder. It only manages things in the AddOn folder currently. Although there is a bug with SavedVariables in ESO's latest update.
Looks like the log you attached shows lorebooks & skyshard being installed? Is this log after you restarted and installed lorebooks & skyshards?
Code:
<message> ESO-1 ++--> LoreBooks</message>
<message>ProgressMap changed for 'LoreBooks' in ESO-1</message>
<message>ProgressMap changed for 'LoreBooks' in ESO-1</message>
<message>ProgressMap changed for 'LoreBooks' in ESO-1</message>
<message>ProgressMap changed for 'LoreBooks' in ESO-1</message>
<message>ProgressMap changed for 'LoreBooks' in ESO-1</message>
<message> PostDrain drainList ***-----> LoreBooks</message>
<message>Download request for LoreBooks</message>
<message>ZipEntry: LoreBooks/</message>
...
<message> ESO-1 ++--> SkyShards</message>
<message>ProgressMap changed for 'SkyShards' in ESO-1</message>
<message>ProgressMap changed for 'SkyShards' in ESO-1</message>
<message>ProgressMap changed for 'SkyShards' in ESO-1</message>
<message> PostDrain drainList ***-----> SkyShards</message>
<message>Download request for SkyShards</message>
<message>ZipEntry: SkyShards/</message>
Thanks for posting your log and I'll run some tests as well on those two addons.