Let's take a step back and look at what you are trying to do here as a workflow. Then we can provide you with possible solutions to your problem.
I'll restate what I've read:
You are using a "phantom" file as connection point for your product. Since this is a customer connection you need to be able to adjust the customer connection points.
There are several options that I think you can look at inside of NX.
1. Use the Part Family template. This is a spreadsheet driven file that controls its children files. You can populate the spreadsheet on the fly and build the child component or
You can prepolulate the spreadsheet and NX will build the child files as they are needed or
You could tell NX to build them all.
2. This might work as a User Defined Feature as well
3. Maybe even the Reuse Library
4. Product Template Studio
5. Just a simple parameteric model that can be changed on the fly- possible using file properties. I think John B. has a YouTube video on that option. John?
Unless there's an infinite number of sizes, a Part Family would still be the preferred approach, just that the Component in the assembly would be there for 'reference only', which is not a problem.
That being said, you could always create a fully parametric version of this model and use that part file as your Assembly file, simply editing the expressions until you have your desired "ambient or dummy part" and then add and constrain the rest of your Components to it as if it were a Component itself. Just do a 'Save-As' when finished and you're good to go. Note that it's perfectly valid, when working in NX, to have both parametric models and Components in the same part file. And you can constrain Components to a solid body just like it was a Component in an Assembly.
If you're talking about taking a 'dumb' solid provided to you by you customer via IGES or STEP or whatever, it's possible to make it parametrically editable by using Synchronous Modeling techniques. However, for things like the number, size and locations of holes, you might be better off, removing the original model faces and adding newly created, fully parametric hole and pattern features to your dumb model. With a little work, it's possible to get a fairly usable 'paramertic' model made from a 'dumb' solid model.
"What we have here is a failure to communicate". I'm beginning to suspect that what you're calling 'Defomable Part' is what we would use Synchronous Modeling to accomplish in NX. Could you perhaps upload one of these 'dumb models' that you're having to work with along with a description of what aspects of it that needs to be updatable?