Some facts which may help you understand it.
1. The same logic or function can be implemented by different cells, For example, ~(A+B) can be implemented as a 2-input NOR; or 2-input OR plus INV; or 2 INVs plus a 2-input AND. These combinations are the same, but have different cell counts.
2. The driving strength of cells can be different and this will affect the area. For example the 4x INV is larger than 2x INV
3. To reach the timing constraints, the synthesis tools can duplicate some cells to reduce the fan-out counts of each cell, which would make the circuit faster.
Back the original question:
Usually the same cell in 65nm lib is faster and smaller in 90nm.
First we assume the netlist is exactly the same in 65nm implementation as in 90nm.
The area of the 65nm is smaller as every cell is smaller.
Now we can think about the clock period. As the 90nm implementation already meets the constraint, so the clock period in 65nm is smaller than constraint (obviously).
The synthsis tool will always try to use less area to meet the constraints. Therefore, the result netlist in 65nm will be different, because the synthsis tool tries to use even less area to just meet the timing constraints. (here may confuse you.)
For an example:
Assuming in 90nm, your circuit run to 100MHz, area about 1000um^2
in 65nm, if the netlist keeps the same, the frequence can be around 120MHz, and area is about 600um^2
As the synthesis tool tries to reduce area while keeping satisfy the timing constraints,
Finally you may get a different circuits of 100MHz with area 400um^2