In most cases, no. There is no difference. They do the exact same thing. However, if you have a variable with a custom setter, then setting it from the script that has the variable will be different.
extends Something
var example = 0 setget set_example
func _ready():
example = 1
set_example(1) #This'll print something.
func set_example(value):
example = value
print("testing")