It might depend on where you work, but I have been practicing in the U.S for almost 10 years and I have always treated based upon my objective findings on evaluation and the patient's goals. Often times referrals will simply say "Evaluate and Treat" with the diagnosis listed. Some docs in my area will write certain modalities in on the referral, but I just write what I plan to do into my plan of care and send it back to the doc to sign off on. The only time I am treating based upon doctor preferences is when I am following a surgeon's post-op protocol, and even that leaves room for variation.
This misconception might be based more on direct access. Most states have direct access for patients to see a PT without a referral, but often insurance will require a referral in order to reimburse - so if the patient wants their insurance to cover their PT, they need a referral or prescription. Hope this is helpful.