Phil 100% means that she is everything to him. He has lost everything and everyone important in his life that he placed value in, and she is the only person who stuck with him throughout it.
Early on, he lost his parents. We don’t know much about it but they aren’t around anymore like Melinda’s mother is. He would have separated himself from childhood friends and family when he joined the academy, to minimize everyone’s loss. Saying goodbye to his best friend from his childhood and teenage years would have broken his heart, but he would rather that than leaving without saying goodbye. He’s kind like that.
Imagine Phil saying goodbye to the other set of parents who raised him. His best friends parents, telling them not to worry about him. They cook him one last meal for dinner because they always thought he was too skinny, and they tell him he’s always welcome. They watched this boy lose his mother and his father, but he’s finally found his true calling and they’re proud.
When he died he lost Audrey, every agent he’d trained, the friends he’d made in the academy (minus a few with high clearance), The Avengers… the list goes on. Most people he’d known, he could never speak to again and it wasn’t his fault.
Then Hydra becomes an issue and he loses more friends than he can count. Fury leaves him. Garrett betrays him. The young man he saw some of himself in betrays the new family he’s made. Everything weighs on him because he has to be in charge now. He only ever wanted to be an agent.
Flash forward and Jemma gets taken. Fitz is losing his mind trying to save her and Coulson can’t do much to help. He’s too busy. He finally loses Fitzsimmons as they mature into adults who barely need him. He feels like he betrayed Ward. The boy who needed the most help. If only he’d gotten to him sooner.
Skye is gone and Daisy appears. Daisy leaves him again, she decides she can’t lean on him for support and he’ll never know why.
They’re not trying to hurt him, but every time one of them is in danger, every time one of them needs a break, it kills him. Why can’t he have one constant in his life? He’s lost so much, given up so much for this.
And then he looks over and sees Melinda. He can always rely on her to be there. She didn’t give up on him after he died, and she’s been his best friend since he left college. If he doesn’t have her with him, then all he’s left with are memories of people he once knew. He’d have no one to lean on. No one to share with. No one to care for. They need each other. She is his whole life because that’s all that’s left for him. Everyone else moved on without him.
So you have thought about it. Interesting. You’re the one who’s always getting out of that shower in that little towel, Jess. Or you’re wearing your glitter or your pantyhose. They’re driving me crazy! Okay? I know how hard it is to get those pantyhose up, and I just… I just sometimes want to rip ‘em down.