I think mostly was resolved in the end. The only loophole is mo xanyu is the key element . There is a artist that draw a good story of why mo was treated like that and why he sagrificed his body. This artist really got a got plot that it really might had happened that mo had found the secrts and was accused of seducing yao to get rid of him
There can be potholes, but all the questions you asked actually have answers. Sorry I couldn't answer it one by one as I'm super busy. But, just wanted to let you know so that you can read it again if you like and check it for yourself. Sometimes the implied ones are the correct answer (Author question answer confirms it).

'This novel had numerous foreshadowings, plot holes everywhere, one mystery after another, layer upon layer of confusing red herrings. The result was that in the end – not even a single one was solved!"
The feeling I got after finish reading the novel
I must miss something while reading the novel because I don't understand :
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SPOILERS
Ok hurm let say....
1) I don't understand Nie Huaisang motif.
We know his the masterminds releasing his dead brother left hand to Mo village (using other hand to kill other),but how he know to get left hand to start all this scheme?
I though Jin Guangyao hide ALL body part somewhere.
And why the heck he split the body into lots of part? For what??
And why he let Xichen kill Guangyao??
How he know his brother death related to Guangyao,has he seen something???
I thought he have a very bad relationship with his brother?
Does Nie Huaising have greater ambition? Since people thought him as useless leader, after reading the fight at the temple, he have potential to become next antagonist...
Actually, I feel he can become next villain when I see his action using Xinchen to kill Guangyao but to my disappointment, no more progress after that (except the extra)
2) did they destroyed the tiger seal? I think I must miss something after the temple to not see what happens to the seal. Sure Jin Guangyao say the thing is now useless....but wei ying didn't see it become useless iron. I imagine is just excuse from Wei ying take the seal back
3) and we see Xue Yang still alive when they fight at the ghost village (that Nie something use teleport) why didn't he appeared at the last fight??
But all in all....love the extra chapter. I'm glad is end in happy ending