What invisible cargo ship exists in the 2 mineral system on the edge of your empire that's so threatened by 2 hyperlanes instead of 1 that it reduces the research efficiency of your entire empire?
All these justifications make a lot of sense for a system that's not in the game, although the game might better off if it was.
It's all abstraction, but it's probably assumed that it's a matter of government resources being finite. The government can spend more on system patrol craft and monitoring facilities to watch the extra hyperlanes, or it can spend it on research. The mechanics don't
directly simulate that, since it should probably be represented as a penalty to research and unity instead, but it's kind of an academic difference.
System patrol craft aren't simulated in game, but there is mention of conflict on the edge of empires that falls below the resolution of combat simulated in game. If you border a marauder empire you can get events related to it, even if you've never actually had any direct combat with them.
I do feel like there's probably a better way to keep large empires from massively out teching smaller neighbors, but this works well enough for me I think. A system more like CKII (and probably other Paradox games) where technology diffuses through territory naturally would probably be a solution, except it's hard to model that in a game like Stellaris with its discrete technologies.