-Confirmed-

Not only is the docking beam hitting docked entities behind the mothership, but the core beam is able to activate logic behind it as well.

https://youtu.be/cleN-vdr4YQ

Further testing reveals that cannons and damage beams also bypass mothership to hit docked entities behind it.

https://youtu.be/lOmD5wwfDp8

This also applies to power supply and shield supply beams.

This needs retesting, seems most beams can't hit most targets.

It's an odd bug that doesn't always happen. You can see it easily on planets though if you fire long enough. It also applies for cannons, missiles and pulse but that's sometimes harder to reproduce. Everything mentioned below is done with damage beams.

If 2 entities overlap each other from where you're looking (raycast goes through 2 entities or more) it will almost always think you're aiming + shooting the one behind the entity you're aiming for. You can easily see this with 2 planet plates near their border.

Gif: I start shooting the planet plate on the left (you see damage, debris helps as indication), I start aiming on the other planet plate but the game thinks i'm still shooting the one I started on. I'm still dealing damage to that left plate but I'm obviously shooting through the right plate because of that.

The beams in my testing, will hit the first entity of a type in its path.

for example, I use power supply beams from docked entity on my ships. The beam will pass through the ship and effect the next docked entity instead of the ship. But when a ship crosses into the path of the beam, it will ignore any docked entity and the ship its docked to and effect the other ship that has crossed into its path.

in current live release.

Since the other ticket got merged with this one since the last update the power supply beams are now passing through a lot of entities.
Before 0.19476 the power supply beams were mostly hitting the first block in its way. Sometimes I would see what I assumed was a graphical glitch of the beam passing through the ship but it was very rare even with 96 x 2 alternating power supply beams.
After update 0.19476 I'm getting power supply beams on docked power modules passing through up to 2 sections of main ship (1 section is 40+ layers of jump modules), 2 sections of a docked shield module attached to the main ship only to hit a 3rd section of the shield module. Also sometimes pass through all of that to hit the forward docked weapon modules. Approximately over half of them are passing through at least two sections of main hull.

Some are stopping at the first block of the main ship or shield module they are running through but its completely random by the looks. The same power supply beam will hit the same target per cycle of ticks. But the next activation will randomly ignore various entities in the way.

One other thing to consider, the mother ship can fire through docked entities.

This will lead to problems where the mother ship falls below 50% shields and attempts to use positioned shield supply beams to protect a docked entity exposed to the exterior.

Another problem would be you are in a turret that overheats and the mothership is firing swarmers, you are inside but the swarmers pass through the wall to kill you.

Not sure if that warrants its own bug report or should reopen this one.

https://youtu.be/-UKZXJWAZHk