I think there is a bit more to the issue then just that the NPCs also explore. To be clear, I think the idea of the raiders is good. I just think the execution is sub-optimal. A non-TN start with reduced population and limited infrastructure (research facilities, etc) means you take the better part of 75-100 years to achieve what a TN start gives you. How fast depends on your starting scientists but it is still not a short time. If you turn up the cost of research, you get much the same result. To have 60 ships show up, that is not something I think anyone in this situation can deal with. They have a 4K speed, my fighters don't even do 2K...I did manage to sneak a squadron in; but they didn't hit anything before destruction. My frigates do 800 kps, admittedly they are using 75% max engines as I didn't want to develop two engines and my survey ships need efficiency. But the kicker is the 325K in ground troops, assuming that is an accurate value, and if I go with the 51K ships being transports it is not impossible they had each 16K or so...that is 10x my homeworlds ground forces and 100x my colony.
I don't really see any solution beyond turning them off at game start. Basically, that single ship can destroy my entire navy, and all my StO's...it will take damage, but it outranges most of my weapons...only the AI's lack of tactical ability could save me...or its weapon breaking down given the new mechanics.
Added in edit: the change in 2.2 will reduce the chance you get the situation I am in (60 ships showing up) but the real problem is that 1 ship is sufficient to destroy my navy, if handled well. The AI won't likely do that given it is currently futzing around but even that kills the game due to being stuck at 5 min turns. For me anyway it is a case of: "it looks good in theory, but works like spit in practice."