You know how when Deus Ex 3 first came out, it had boss fights that you couldn't get around, you were just forced to fight and kill a guy? And everyone was mad? And later the devs patched in other options, basically one for every style of play you might be into?
Well I've decided they were right the first time
A video game typically has a design contract; a set of rules that aren't explicitly part of the game's mechanics, but that constrain the content (=level, quest, world, encounter, etc) design of the game.
For example, Mario levels don't contain gaps that Mario can't make with a jump (unless there's some special level gimmick or circumstance). In fact, normal Mario levels are typically completable without running jumps.
Deux Ex' design contract is very small and abstract: levels are constructed like real places and follow real-world logic. DXHR adopts a totally different design contract: levels support every 'playstyle pillar' available. This absolutely leads the game towards feeling very sterile and artificial.
I do think though that you can adopt a similar contract and not run into those issues, you just have to think more, uh, thoughtfully about what those pillars are. In DXHR et all they are themselves very narrow. Compare this to Dishonored, which has basically two 'poles' of action: Stealth/Combat, Covert/Overt, Restraint/Chaos. All the abilities and verbs the player has are grouped into these two clusters, and there only being two makes it much more reasonable for levels to consistently support both. There's always a stealthy path, but the game isn't compelled to let you access every space through any given tool, and the game is allowed to tempt the player with the grass being greener on the other side: some spaces favor the covert approach more, while some lend themselves to chaos.
However, this is also why I think the boss fights in DXHR are problematic. The game is ultimately breaking its contract there. This is something you can do (Fallen London does it in a certain storyline, for example), but you have to do it in a way that's thematic and satisfying; and DXHR did not. It simply drops its design expectations all of a sudden, leaving it in a no man's land; it's neither committed to the new, all-paths-are-always-valid design language, nor to the old bottlenecks-exist design language.