Shouldn't be a problem.
Latisse was not specifically studies in patients with tattooing or permanent eyeliner. It some individuals, it can darken the skin. For women, especially, this may actually be beneficial because in this rare occurence, it can mimic brown eyeliner.
Of course, you should not apply Latisse on any open wounds, inflamed or irritated areas, which includes your healing period after having micropigmentation or permanent makeup.