Hello!
I am so sorry to hear about your tight Achilles, that sounds pretty terrible. I have had many different tendonitis over the years and still have to loosen up certain muscles to be pain-free. Doing a long warm-up both before you get into your workout as well and easing into training does help. I have always had lots of success figuring out what is causing the tightness, usually what is hurting or is SUPER tight is a reaction to other muscles being either weak or out of line. For example, I had extreme elbow issues due to my shoulder blades being too weak and not functioning properly. I had foot pain that took over a year to heal due to my entire leg from my hips down being too tight. I still take stretch breaks all the time to keep my feet happy.
I am not a PT, but I would focus on full-body mobility! Nerve flossing too might be worth a google and a try for you. I have had lots of success (as have other athletes) in helping loosen up their legs. I am not knowledgeable in specific ankle mobility but I do think there are ways to fix these issues. It sounds like talking to another PT or going in with the focus on your Achilles might be in order!
I hope that helps!
Maya