Hmm, well. Not being able to buy the master spells is a problem I personally encountered on several playthroughs but when I searched the SkyRe thread I only found a few other people stating they had the same problem.
https://forums.nexusmods.com/index.php?/topic/563161-t3nd0s-perk-overhaul/page-2968#entry8377531
It's not that SkyRe is unusable, it's just that certain spells or perks don't always behave like they should or don't work under certain circumstances.