Yeah it kinda does.
I tend to think the entire point of the Find Shaun plotline really amounts to nothing more than a vehicle to meet all the factions. The main plot nudges you towards concord (minuemen), then the BOS airship shows up (BOS obviously), then after that whole mess with virgil and the courser, you have to find the failroad, then finally ending with the institute.
After that, the Shaun plotline simply vanishes into thin air. I know, the plotline should end with finding shaun, but there's really no closure to it. No epilogue. Throughout the whole game, your character won't shut up about finding your son. Everyone you meet (preston, Danse, Piper, Valentine, Virgil, etc) the first words out of your mouth is "AH GUTTA FIND MAH SUN!" Yet when you actually do, it simply stops and no one ever brings it up again, as if your whole search for your son was one giant big lipped alligator moment.
It's like the game basically says "Okay, here's your son. Now shut up and pick a faction already."
Your partner doesn't comment on it. Piper at no point says "Soooo blue, last I heard/seen of you, you waltzed right straight into the den of evil itself. I thought I'd never see you again, yet here you are. Mind letting me in on what happened?" Danse or Maxon never says "You've returned from the nest of evil itself. Tell me about what you saw. And did you find your son by any chance? I can only assume the worst since I don't see him with you." Nick never says "Well, you managed to waltz right into the boogyman's house yourself. Yet... your son. He's not with you. What happened? Don't tell me, he's dead, isn't he? I'm here if you need to talk about it..."
Even if you take them to shaun himself after the Battle for Bunker Hill, no one comments on it. Piper doesn't say "Wait, THAT was the Director the institute? Right in front of us? And your son? Never saw that coming." Danse doesn't make some allegory to Cutler, Nick doesn't say something like "So that was your son, huh? Talk about one awkward reunion, for the both of us."