With "être + adjective" (or a noun that adopt an adjectival syntax for this particular construction, like with occupations), il(s)/elle(s) is used when the subject is 1. a Noun phrase or an independent pronoun and 2. specific.
In all other cases, ce is used: infinitive (se réveiller, c'est dur), subordinate clauses (que tu te soies réveillé, c'est bien), quantified NP (Quatre repas par jour, c'est beaucoup), partitive NP (des chips, c'est pas nourrissant) generic definite NP (l'hiver, c'est fatigant - that is, winter in general, rather than the particular winter we're in) and so on.
It has nothing at all to do with gender.
In the case of sentence in the question, we could rephrase it as "J'ai une autre voiture, mais cette autre voiture est bleue". Since "cette autre voiture" is both a noun phrase and specific, we have to use one of the +specific +NP pronoun, with the right number and gender agreement, that is to say, elle.