Vanilla now have 3 types of command blocks, but only one type of command block minecart. Railcraft can add the other two, repeating and chain command block carts.
Repeating one will execute the command every tick it is on the activator track kit.
Chain one can be done through cart linking(adjacent command block carts' execution) or through some sort of detector.

The existing impulse one may be replaced for supporting the chain command block.

The Repeating Command Block is the current behavior of the Command Block Cart. Changing the Vanilla Command Block cart's behavior is a breaking change, and should not be done.

We can simply use registry substitution.

Again, that's a breaking change for existing maps. I personally see no reason to do this.

well, railcraft also replace other carts, and uou can say it is breaking...

Except Railcraft replaces those carts with an equivalent version, and they don't really do much. Replacing an entity intended for adventure mode and servers that has special behavior to support that usage with an entity with different behaviors strikes me as very bad.

They will have the exactly compatible behavior, but the texture might change.

Its implementation will be like https://github.com/CovertJaguar/Railcraft/blob/mc-1.10.2/src/main/java/mods/railcraft/common/carts/EntityCartCommand.java, extending the vanilla class directly. Pinging @CovertJaguar for opinions.

Command Blocks confuse me.

@CovertJaguar How do you think of this after all? I think I can all three types of carts, just change the chain from block forms to cart linking forms.

All I know is that it breaks peoples scripts right now.

Honestly, we cannot add command blocks directions in until we have better control over the link direction and minecart direction in general.