I mean could you realistically expect 400 scenes to all be tied into the main narrative somehow? I can't imagine trying to script that into like every sidequest or planet, and not expect things to go wrong.
Also not every scene is gonna appeal to everyone, so I'd hate to see the scenario where someone puts work into clearing a quest, just to get a scene in a genre that they never liked.
It might irritate some people, but I think this was the safest way to do it. You unlock what you want to see, you're never tricked into viewing something you didn't want to. No mantic dick is shoved into someone's face unless they specifically go into the Xeno category. You don't like futa, avoid that section. But I wouldn't tie that into the main game, cuz then what does that do for other playthroughs, you're essentially telling people to not go through certain parts because it'll lead to things they're not into.
Scripting scenes into the story would be simpler if it were say just the captain and the ladies. That's a much smaller field to deal with. You could get that from say Treasure of Nadia, lots of scenes with lots of ladies, but its only ever just the one guy, so that's a simpler focus.
Really the simplest way to explain Pandora is that its all the boning the crew gets up to during all the time the story takes place. Its mentioned in Killi's recruitment quest that the treasure map hunt took a number of weeks. There's no exact timeline, but its a lot like any RPG where you can spend hours doing things but in-story its been months.
In the end the scenes that are in the main story are the ones most relevant. The recruitment scenes when they're brought on the team. Ela, Taron, and Sova's stories were worked on to be more promiscuous in response to early feedback. And through playtime the relationship with each lady grows, and culminate in personal quests that'll end with cinematic boning, which as I've mentioned before are meant to be several minutes long. Multiply that by 10 and you gotta see why they couldn't just apply this to every scene, and make everything premium level, with everything having a climax, with a limited budget, and team members that are not gonna be around the development forever.