I think because everything relating to the brackets and fasteners is within parenthesis, apart from the hardtop, that it is pretty clear that "it" refers to the hardtop.
Not to mention it'd be grammatically incorrect to refer to latches, fasteners, and mechanisms as "it" since they are plural. If you are going to bother to rewrite it, you could just have:
Cars may compete with the Mazda factory detachable hard top in place, but it is not mandatory. If equipped, latches shall be replaced with positive fasteners and rear pin attachment mechanisms must be used or
replaced with positive fasteners.