On the ship, Paul went against everything Midoriya believed in. Midoriya would have stopped him by force without hesitation if he had been able to at the time. Now Paul comes to his defense against the fear that Midoriya will be seen as weak, in a reflexive manner imprinted on him by how he was raised, as if that vigilance will protect anyone from the pain within.

It's Midoriya's kindness that gives him strength, not weakness, but it hurts so much.

He still feels terrible for being a bother when he originally came along to help. Instead, he failed to get Kaworu to leave with him, and now he's crying in the back of this man's truck. With Paul so close, Midoriya's body expects to be enveloped in the arms of someone who loves him. (And Paul still loves him, or he would not have spoken these things at all.)

Inertia wins out. He doesn't want to get into it with Paul here in front of poor Daniel, because he doesn't know if he will hurt Paul with words or--what he wants more--weep in a clutching embrace unable to let go. He wraps his arms more securely around his buried head as if that will make up for the absent hug his body craves. He has told Paul this very thing, that it's okay to cry. Midoriya tends not to hold things in. If he does, something is terribly wrong, and there are too many things wrong already today.

He does as Daniel suggests and lets it out.