There is no way to make transit tubes cross ladders.
There is no good way to get around this without making your base janky and ugly. It's a terrible design decision to force players to make their bases janky and ugly if they want to effectively be able to use both transit tubes and ladders in their base. Honestly don't even want to keep playing the game after finding this out. Duplicant commute times are way too long without using transit tubes, and since there's no good way to incorporate them into a base if they can't cross ladders (without completely designing a base around them and causing an over-reliance on keeping transit tubes powered) I'm just gonna give up on my current game and play something else. Such a buzzkill to get to the point where you can use transit tubes in a game only to find out they can't cross ladders. Hope this gets fixed in the future so it's actually possible to make a decent base. Until then I have zero urge to keep playing this or to recommend this game to a friend.
Such a simple fix that would lead to a huge quality of life improvement for players.
1. Build a ladder.
2. Can't build transit tubes that cross that ladder.