I found a fix for my Gardener of Men glitch:
When I first completed the Path of knowledge quest with Neloth and got the black book, I wasn't able to continue to "chapter II" because the platform where the book should have been wasn't there.
To fix that glitch, I had to go back and complete the last part of the Path of Knowledge quest (where you place the four cubes on their pedestals) and re-enter the reading room so to re-trigger the Gardener of Men quest.
It appears that in Apocrypha, certain things only appear when you trigger them by starting the related quest, and somehow this quest didn't open correctly for me and thus the platform didn't appear. So going back and re-doing to end of the previous quest and making the quest open again fixed whatever happened the first time.
My earlier confusion over this glitch, BTW, was NOT helped by geniuses on You Tube who posted edited "walkthroughs" of this quest that skipped over this part. Apparently some people have difficulty with the concept of a "walkthrough".
But thankfully when i re-started the quest, I was able to complete it with no issue. Also the glitch with dragons acting weird when they attack seems to have been fixed too.
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My house has some glitches too:
Like other people, I have a problem with the weapon racks. Many of them don't work and the weapon just falls to the ground.
The mannequin just left of the bedroom door as you enter is glitched. I put my old Elven armor on it and then switch it out for some cultists robes But now, no matter what I put on it, it generates new cultist robes, gloves and boots (but not a helmet). I think I ended up with 8 of each before I just gave up (at least I got some coin for them!). The armor I place on there doesn't disappear--it's still there, just not equipped.
The chest in the main bedroom that's on the bottom of bookshelf generated filled soul gems: I placed 4 filled Common soul gems there. When I came back for them, there was 14. Sadly this appears to be a one-time deal unlike the mannequin.
When I first put a set of carved Nordic armor in the chest at the foot of the bed, it generated a second one. Also appears one-time only.
The safe in the bedroom generated a second Ring of Eminent Conjuration when I placed one in there. I suspect it's generated a few other things too. However, I use this safe for any jewelry (necklaces, rings, circlets) that I've been collecting and I can't kept track of what all I've collected. But there's a few things in there that seem "new".