One-point on the idea of species specific techs. there are two ways that the idea could be implemented without being directly species specific
1. Techs that replicate a species pick ie Tolerant/Core Waste Dumps from MOO2... a Tolerant species doesn't need them... because they naturally have that ability.
2. Techs that have differing effects based on what your species picks are, ie species inbuilt Ethos will affect the happiness of implementing certain government techs.
As for Rebelling... if a true multiplanetary organism is going to have rebelling planets, then I think it should be random which ones rebel... ie every planet you have has a X% chance to rebel based on various stats.... of course, using the mental breakdown model, reconquest wouldn't mean that 'all is well' instantly, reintegration would take time. (it may even take some of those techs to 'make' a higher level hive mind)
Ideally in a game there should be no % chances of things happening, but instead real cause and effect reasons behind why something happens. I imagine that this would also allow players to see why there planets rebel and give players the ability to prevent rebellions.
But there can be good reasons, eg distance from homeworld, lack of food, supply problems, crime, policies. I could see a % chance system coming into effect more to decide when a rebellion will occur, as given a good reason, if a rebellion is to occur, it would be uncertain if it would happen today or next week. If a rebellion would occur is not so much chance, but what has happened to lead up to this, eg for the last x turns the planet has had no food supplied.