Yes, they definitely get better.
If ultrasound and laser were irritating your symptoms then likely the condition was fairly acute...i.e. fairly inflamed. In which case, it makes sense that deep massage would continue to irritate it.
In the case that the affected structures are inflamed, they need to calm down before moving on in the rehab process. Unloading these structures is important which is basically what you are doing with orthotics (and activity modification which your podiatrist should be able to help you with as well).
It really sounds like you're on the right track. Try to be patient but also stay active with this rehab process (keep asking questions; make progressions as possible based on what you're advised to do)
I would encourage you to consult a physio again as things settle down. Not necessarily for deep massage as you mentioned but for a full assessment of your back, hips, feet etc. It's important to know how to prevent it from recurring and quite often the answer is not actually just in the feet.
Good luck!!