I'm not sure exactly what your consultant is advising you to do, but my understanding is you have to treat your design (the tool) and establish a process to ensure the design meets the intent. Yes, if you design the tool, 4.4 applies.
APQP can be applicable to some extent. Unique designs (also called one-offs) may have less applicability than, say someone producing cutting tools or even, for example, larger equipment such as screw machines, where you can have the same checks being made on each production run. Your
FMEA can look at previous builds of similar product and "things that didn't go right" for ways to improve lead time, etc.
So if you consider things like how you conduct design reviews of your tools, how do you verify incoming material, how do you verify your assembly (could be the same PCP for many tools) and what is your final inspection, you can apply some of the techniques of APQP. If you look at the intro to T/E, "implementation" section, it does say that "it is recognized that not all of these requirements are applicable to every organization" - (then uses the obvious example of Element 4.4). However, if you determine something is not applicable, be prepared to justify why. Make sure you think of all angles, because your auditor will.