I'm not sure what exactly your argument or stance is, here...?
The Synthetics perk line has a direct connection to the AI Rebellion crisis because it is focused on replacing your population with synths- production of robots, droids, and synths is closely associated with the AI Rebellion crisis. Whether or not taking the perks makes triggering that more likely or not isn't something we know yet- we don't know how any of the Ascension paths interact with the Crises- but we can quite reasonably speculate that there will be some form of interaction because of how closely related they are.
The Psionics perk line can be interpreted to make reference to the Unbidden- I rather hope it isn't, and that there isn't any sort of direct link between them, but I can see why people would speculate.
The Genetics perk line has no such close association or potential references to the Prethoryn. Nothing in its descriptive text alludes to them, and there's no reason to think that increased genetic engineering of your species would create the Prethoryn- the Prethoryn are a distinct extragalactic group with no prior contact with the Stellaris galaxy that we know of, and as far as I'm aware, no indication that they were created through genetic engineering or are the "inevitable" result of such.