I don't like key hunt missions.
I don't like when previously non-existent enemies appear when you trigger something.
While this mission have all those two aspects above...... I can't help, but admire it anyway - since this is an expertly crafted mission. Varied areas, interesting enemies, lots of great details everywhere! One of the greatest strengths of the mission is the pacing though, because while the map is pretty big, it is surprisingly well designed.
Seriously, missions like this are the reason why I enjoy fan contents much more than the original Thief campaigns.

I like that keys here (except for runes) are just optional and mostly just simplify our traversing through the locations rather then being essentially needed.

Yes, absolutely! Also, I think what makes the pacing really great in this mission is the fact that you have to unlock the different areas one by one - so, it doesn't just throw you all the map at once. Lots of levels go too far with the non-linearity and all the different routes, but Nick's approach here was actually quite clever.