I don't work for ESRI, so just my 2 cents worth, but a couple of things to note:
- Vector tile support, and vector tiles themselves, are still kind of in their infant stage. They haven't been around that long compared to other data formats.
- As a consequence, there a still some clear limitations, e.g. in the symbology that you can use.
- As far as I understood, yes, vector tile packages are not really "designed" or thought of to be "re-packagable" in the way you desire, like a random zip/unzip operation, with modification in between. I think ESRI, and many other companies like the original designer of the format Mapbox, that are supporting vector tiles, mainly think of them as a handy "create-once / style many" format. That is, you don't change the contents, just re-style by slapping on another JSON style file to get "another" map.
- I really think your current use-case is marginal (both in terms of current users even remotely attempting this, and what chances there are of ESRI supporting this in the near future).
- Then again, the vector tiles and support are likely still very much in active development, you never know what the future holds.
By the way, what is it exactly that you try to do? What modifications are you making to the unpackaged content?
I see you mentioning the need for "smaller areas", but is that it? And if so, why do you need it? I also think Vector Tiles are not designed as a distribution format if that is what you attempt to do, for that, create a Map Package (.mpkx - Map package—ArcGIS Pro | ArcGIS Desktop ) instead. Vector Tiles are designed to be deployed as a vector based webservice on e.g. ArcGIS Online, where your users generally should not care about "extents" of the data, as they simply zoom in / out to the area of interest.
If you do attempt to use it as a distribution format to send off to some other office / department, then remember the vector tiles do not contain the full quality of your data, nor content, and are cut in tiles, all of this may hamper subsequent usage by your "clients". Again, use a Map Package to distribute true original data including styling and all.