I managed to clip in and out of the Helicarrier. Further more, I found a use for it for speedrunning! (Skip to 9:20 if you just want to see that)
1:30 - I squeeze between the tube shape and the wall. Some ground in that spot isn't solid, so you clip downwards. This allows you to travel inside the Helicarrier. You can't web swing inside and there are only a few spots to web zip to, so kick-fly is the best method to maneuver around.
This is why I took down some enemies first, so I won't web-strike them by accident when using the kick-fly trick.
It's very easy to clip out of the Helicarrier, so be careful.
2:00 - This is where the cutscene of planting the first bomb takes place at. There are invisible walls the prevent me from moving away, so you have to reset the mission.
4:05 - I managed to ascent into the missile room. As expected, neither the enemies or the missiles are loaded, so you can't progress the mission without destroying the generator first.
5:00 - To clip back out of the missile room, push against the wall behind the big missles. If done correctly, you'll be pushed down between the missiles and the wall. Simply walk towards the wall to clip back outside.
I continue the mission normally for a while, you can skip that part if you want to.
9:20 - After I grab the bomb, I clip as I did in 5:00, which leads me directly to the bottom spot where I plant the bomb.
I estimate that if done right, this can save up to 10 seconds. I think it's worth the risk, since it's not too hard to perform this trick.