Just separate these outputs, as it will be better. Or it will make it less balanced?

I don't think it's possible to separate them using normal combinator prototypes as the basis of the computer entity. That's why you have to place separate additional combinators to get more inputs.

You can use extra normal combinators outside the computer and use bit operators to unpack more signals sometimes.

Place additional output to combinator (introduced in 0.4.0) and use it instead as one-color output.
There is a way to make red and green outputs independently controllable (if you mean this), but only for bigger version of combinator, and it will make usual output (with same red and green signals) twice slower. So just use additional output entities.