Too many biter types completely ignore walls when shooting projectiles imo.

Electrical, sapper, and fire bugs just shoot directly at turrets and other buildings behind walls. They also have AoE attacks that quickly damage a lot of structures at the same time. If there is a decent amount of them, turrets will explode within seconds of contact. Electrical in particular are incredibly strong, they appear super early in the game and a swarm of them can one-shot any defense setup instantly.

I have a mixed defense of laser, gun (with red ammo) and flamethrower turrets, but they constantly penetrate my wall and cause carnage. There is no counter to this, besides massing so many turrets that they die before even getting in range, but even that often fails, and it's not sustainable either.

I'd think it was a skill issue / too many biters / too high difficulty / not enough turrets kinda problem, but the other types of biters (acid, fast, suicide, laser, regenerative, spawner, armored, wasps etc), while still dangerous and strong, cannot penetrate a fully built and supplied layer of my defense.

It would be nice to have an option that makes all enemy projectiles collide with walls, just kill Combat Mechanics Overhaul (or alternatively, make it compatible with CMO)

Fire, electric and the like are designed to destroy defenses behind walls. This is how it is intended.
Walls significantly reduce the danger of biters, but will not protect you from everything. You need to learn to deal with them

Also, in the late stages of the game you must have the ability to automatically restore destroyed defenses or you will lose

Back in 1.0, you used to have the option to use Combat Mechanics Overhaul to force biters to have to destroy your walls before this mod became incompatible. If you're having trouble keeping your turrets alive, it might be better to look into mods to buff your turrets.