That is similar to how P&N tried to have training facilities work quite some time ago. In addition to not stacking, the highest ability level of each type is used from all facilities on the planet. So, having a 3/turn to max 10 facility and a 1/turn to max 20 facility ends up with training of 3/turn all the way up to 20.
You could use the system training ability to get 3% up to 6%, and then use a planet facility to do 1% up to 20% or whatver. Might want to make the system one do 2% per turn, since one system and one planet training facility do add, so you don't want to get 4%/turn accidentally.
