I'm not sure if this is a bug or intended but today I saw an enemy move their units through one of my team's teleporters. It happens at about 18:50. Here's the link to the game on pastats. http://pastats.com/chart?gameId=212942 Thankfully his units killed our teleporter before his vanguards made it through otherwise that commander on the metal planet likely would have died
It's intentional. Propably have to set your units to "return fire" to avoid it attacking the Teleporter. And since it is yours, you could just turn it off.
Com-napping used to be a thing with transports. It was OP in alpha, an astraeus reaching the enemy commander was an instawin and/or a humiliation. Simply because if the astraeus died the commander died instantly, whether you killed it or it self destructed.
Commander napping worked the same way in TA Worse since even if it wasn't game was set to not end when you lost your commander, the commander explosion killed everything in the blast radius. PA's com explosion is much more mild.