This is only their home system, I am not suggesting they colonise any other system. The major races can colonise other systems, the minors can't. They do however colonise there own system.
The minor civs should go through the following stages
1. Coloninise home system
2. Once home system colonised, focus on research and social and militery ships.
3. After a certain point, begin to colonise again, any system can be colonised.
4. Once the minor has no systems left to colonise, focus again on research and social and expecially the production of militery.
This should ensure that minor races are handicapped in colonisation, but in a galaxy where the major races do not succeed in colonising all the planets in the other systems quickly, the minors will eventually do so.
Why are the dark Yor, not as dangerous as the Yor? Agressive doesn't necceserily make a society dangerous. A violent and hostile varient of Yor, could easily be hampered by internal strife, while less violent and hostile Yor, would be more harmonious.