I can't remember if Phantoms can see through cloak on Gold, but I know they ignore you on Silver if you keep your distance. Geth Primes can snipe from across the level with their cannons, but I think they prioritize visible targets if they're unobstructed.
Quick note about Phantoms: if you don't have someone on your team who can stasis, you can cloak, move to a flanking position where the Phantom is taking cover and line up an easy headshot.