The official Car Fax web site states that they only have what is reported to them . Also that wrong information can be reported . They are a helpful guide not an absolute record.
Alignment is not anything to worry about because any vehicle will need one sometime. 40000 miles for brake pads and rotors is not out of line either. You bought a used vehicle plain and simple so you should expect things to be done to it . Tires are in your future also.