I just did BoC for the first time and I had to take 2 pauses of 15 minutes because I started getting real dizzy during the dungeon, something like that never happened to me in any game, maybe is because the dungeon is to dark and has a lot of flashing red things.
I dont know if it was because of my condition or if the enemies are strong but this dungeon looked a lot bigger compare to Steps of Torment, maybe you should decrease the number of monster there.
What, are you saying you have epilepsy? Sounds like maybe they should put a warning saying some sequences may aggravate that condition rather than cutting back for the other people who don’t have a problem with it, no offense. I love flashing lights and crazy effects everywhere 
seems kind of like a personal issue, maybe you should go to the doctor? honestly i dont want a fellow GD player (or anyone really) getting sick while playing.
how long had you been playing up till that point? had you eaten?were you on a laptop or desktop? maybe try adjusting the contrast and gamma and seeing if that helps?
It might be the reddish haze thing. I’ve heard of other people experiencing dizzines/headaches when playing dark themed RPGs with demonic elements (black/red color scheme) especially when they’re tired or sleep-deprived.
If symptoms persist, you should visit a doctor.
And yeah, I think between SoT and BoC (dark background + lots of flashing colors/reddish haze) a warning for people with medical conditions might not be a bad idea.
I get very sick when I play FPS games where the camera moves/shakes really bad. Kind of like motion sickness. Not exactly the same thing you are experiencing but stuff like you describe does happen. Try keeping all the lights on in the room you are playing in.
Your missing the point that these people don’t want to simply stop playing the game they clearly love, and shouldn’t be told to when fixes to both these issues should be a simple Config.txt file away.
Specifically the red flash tied to entities no doubt porting in (I’m a DRM free backer and haven’t had the chance to play the game yet so cut me some slack) could have values for high brightness and contrast with values based of configuration settings; or even a setting to just turn them off if they are linked specifically to monsters.
That camera shake stuff should be a simple 0/1 (off or on) affair. Hopefully once we get modding tools going these will become a reality.
Now I’m not saying it’s the issue you have but (https://www.epilepsy.org.uk/info/photosensitive-epilepsy/triggers) this website seems to suggest the red light is less likely to cause issues if your epileptic.
What this means having known quite a few people with different disorders as i have is that it may not be epilepsy you could instead have dyslexia as blues and green seem to help them focus better while red might give a scattering effect that I would suspect causes for you a bit of registration lag of the image that your brain is trying to put together right and make sense of; with strain as the result.
My other thought that comes to mind is colour shift whereby if you stare at a colour too long it super imposes on everything else, in this instance i would say that perhaps the screen image is creating a central red haze effect that makes the light from the surrounding area less red (like wearing old 3d glasses too long then when you take them off everything has dull colouring), causing sensitivity to the room.
I think if it’s creating health concerns you should have it checked out, but my suggestions as for an interim solution would be to block the red light by configuring you GPU colour balance+contrast and if that doesn’t work try cellophane (ideally blue as it will turn it purple instead the closer to Infra Red brown); anouther solution perhaps is to lessen the impact of the surrounding light and I don’t know enough about neurology & vision disorders to really say whether you should turn up the light, turn off the light, dim the light or even install a red bulb.