Can a PDF be "embedded" into another PDF, and still be its own layer?

HI. I work with a software company that manipulate PDFs files, placing PDFs into other PDFs resulting in a combined file.
what my question is, is the finished combined PDF file simply 1 big PDFs full of individual elements, or are the elements still relating to their own virtual pdf within the combined PDFs?
MY feeling is the combined PDFs is simply a big fish tank full of fish, and if another fish tank was to be emptied into it, it all merges into one. At least that is the way I see it. all fish a simply a part of the overall fish tank!
i Ask this as "a colleague" is telling clients otherwise and I would like to correct him.
oh, we use itext as the tool to manipulate pdfs.
cheers

Thanks for the reply. I understand my wording was misleading.
What we are doing is taking a single page base PDF file, containing 10 elements for example, and using our own software (with help from iText) adding other page elements on the same page. Most of the time these elements are just text, or the odd image, but sometimes, we may be placing a PDF Logo on the same page. The resulting PDF seems to be a single page, containing 10+  elements of equal hierarchy, with no reference to the source PDF file that was used for the logo. Also looking at the Layers panel, There is no information here.
Are you saying then that there may be references to some of the elements based on the source PDF file?
Cheers

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