That is correct.
If it was the power mains in your house, it would (probably) not matter, but here we are talking about devices which switch on and off very fast and in the process create electromagnetic impulses which may affect the sensitive input circuits of other parts. Of course, the mechanical parts of the relays move far more slowly, but it is the electronics that matters.
So the right hand side of your diagram is correct.
As to the pros and cons of a second power supply in your second picture, it may or may not be more reliable that way. I would be even more concerned about what will be powering your motors and the total load on each power supply, so it is a much bigger question.
I saw the matter of pull-down resistor values in another thread yesterday. 4k7 or 10k is of little significance but you should have switches wired to ground and use pull-up resistors. The best value of the pullup resistor will depend on the quality of the switch(!) and whether it is close to the microcontroller or at the end of a longer cable.