This is an interesting question. Take a look at the manufacturer Spinlord. They aren't exactly one of the "big names" in table tennis, but they are big enough that I think we can assume that they follow the rules (and have consulted with ITTF on the rules where necessary).
Spinlord produce a range of different racket covering types, and they have several in their range where it is the same top-sheet but attached to different sponges. For example, there's two versions of the Degu short pips, three versions of the Waran short pips, two versions of the Adler pips-in rubber, three versions of the Irbis pips-in rubber, and four versions of the pips-in Marder rubber! There's a couple more examples as well. Here's their website page:
spinlord-tt.de
However, if we go to the ITTF list of authorised racket coverings we can see that whilst Degu, Waran, Adler, Irbis, and Marder are listed, each with their own approval code, there are no additional listings for each of their differently sponged versions (there is no listing for Degu 2 or Waran 2 etc etc). On the face of it, this would seem to suggest that it is only the top-sheet that is subject to ITTF authorisation, and that once the topsheet has been approved, the manufacturer can attached to it whatever sponge they choose without further approval. However, if a manufacturer were to do that, it seems to me that that would then go against rule 3.4.2.2 which states that
"The racket covering shall be used as it has been authorised by the ITTF...".
So, how can we reconcile the fact that different sponged versions of the same top sheet don't have their own approval codes on the ITTF list of authorised racket coverings with the fact that all racket coverings should be used as they have been authorised by the ITTF? My brain is telling me that the answer to that question must be that all of these different sponged versions
have been authorised by the ITTF, but they have been authorised under the
same approval code as their original (parent) version.
So, if my line of reasoning is correct, then the answer to your question is as follows:
Yes, manufacturers can (and do) produce racket coverings with the same ITTF number but with different sponges, but in order to comply with rule 3.4.2.2 I think we have to assume that each of those versions has been presented to the ITTF for authorisation.
Furthermore, the requirement of rule 3.4.2.2 would seem to prevent an individual player or anyone that wasn't the manufacturer from peeling apart racket coverings in order to make their own personalised mix-and-match versions of topsheets and sponges (unless, of course, it was somehow possible for an individual to get their own creation authorised by ITTF...which seems nonsensical since it would then need to have an approval code which was different to the approval code displayed on the rubber topsheet!)