If a method is patented and to conduct this method, you need to build a device that has been patented in the past although not in the exact shape and form nor for the same use, will you be having limited freedom to operate? For example, if someone has patent the pill, i.e. any chemical in the form of a pill to be swallowed, and someone else patented the use of pills for treatment, while you patented the use of pills for feeding, will you have any freedom to operate?
As we used to say "Do you walk to school or do you carry your lunch?"
The question is a non-sequitur. Being granted a patent has absolutely nothing to do with your freedom to operate. Your patent affects others' freedom to operate. Your patent confers no positive rights for you to do anything.
The only way your patent application process impacts your freedom to operate is since your invention is published, no one else can get a patent. Your invention being published does provide you freedom from a third party getting a patent.
After publication, you getting the patent affects others' freedom to operate but does not change your freedom to operate. If your application was published but not granted you would be in the same position regarding what you might or might not be able to do - assuming a patent was not issued to another in spite of your publication.