Absolutely it was considered scary. It's not very scary any more, because we've all played it a hundred times over. But back when it was first released, certainly.
those were exactly my thoughts when i played doom for the first time. i was 20 then. well i wasn't exactly scared, rather impressed in a way no game before managed to do. before the advent of first person shooters, i always wanted to play a game where i was "inside" the action, seeing everything with my own eyes. wolf3d brought that, i played it again and again, tirelessly humping the walls for every secret. but immersion wasn't complete yet, for the reasons you listed: same light level, orthogonal walls, comic-like graphics and sounds. this broke immersion for me.
then doom came, and i remind us spoiled kids that its 320x200 vga graphics seemed "life-like" back then. i can't forget standing at the green armor in e1m1 looking at those chinese mountains outside and thinking "how the hell did they do this" and "hey, i want to get out there". it was similar to the scene i would watch many years later in cameron's "avatar", when jake entered his clone body for the first time: immersion was complete. i was "in" the world there, right in the action. those hands holding the gun were mine. this was not only because of the graphics. doom had the perfect mix, of sounds, design, and control. hence my preference for (unrealistically) oldschool fast movement and accurate input. modern games are graphically much more advanced, but i don't feel as much "at home" when moving at a snail's pace in comparison.
as for the soundtrack, sure the psx version is darker, but it's also a bit the same, at least to me. add the growls and constant distorted sounds and it gets tiring in the long run. bobby prince's soundtrack has these metal rip-offs, but also more variation.