I respect your experiences with Unity, of course (and my experience with it is exactly zero!), but what about these titles:
Shadow Tactics: Blades of the Shogun
Inside
Pillars of Eternity 1-2
Firewatch
Kairo
Tyranny
Tacoma
Pathfinder: Kingmaker
Gris
Ghost of a Tale
Return of the Obra Dinn
Pathologic 2
Wasteland 2
Might and Magic X: Legacy
Endless Legend
Endless Space
I have played about half of these myself and they are wildly different games, if no one told me they were made with Unity I'd never guess. So the argument that it's not really customisable doesn't hold water at all, in my opinion. Maybe really small 1-person indie operations keep re-using some stock assets or something, but that doesn't really tell you anything about the possibilities and the quality of the engine. Or you're only referring to the scripting? Most likely these games use a combination of scripting and their own lower level stuff, that's true.
Shadow Tactics was a particularly impressive and unique RTS stealth game and apparently they've even used the pathfinding algo that comes with Unity (check out the linked article). Similarly Pathfinder, Pillars, WL2, MMX and the Endless games, they're wildly different and pretty much the AAA-tier of the non-AAA segment, if I'm making sense.
So, without having any experience with Unity myself but having lots of experience with writing my own libraries, it's just huge amount of grunt work and there's always a risk that after spending much time on it you'll just end up with a half-assed homegrown version of what 10-50+ other devs have come up with and polished over 5-10 years. Of course, sometimes it's just interesting work or you just might say, yeah fuck it, I'll write my own anyway because it's fun or I just want to learn etc. You can't always be rational, after all
But approaching it purely from an effort/benefit ratio, Unity seems to be a very practical choice for a lot of non-AAA games, if nothing else. I don't think I'd even try writing my own engine unless I had some extremely specific needs that are just impossible to achieve with it. One thing that comes to mind is streaming a large open-world without loading-screens (like most Piranha Bytes games), but apparently the guys iimplemented something like that in Firewatch:
https://www.youtube.com/watch?v=hTqmk1Zs_1I&feature=emb_logo
I'd be curious about the experienced game dev folks' opinion on this.