See here for reference
An APTX file is just a fancy project package.
As a result, by default, it wraps up and copies anything used in the project UNLESS it is in an enterprise GDB (and possibly a service?). What then happens is that you end up with a million copies of big things like DEMs.
I recently asked about this at the UC and was told that this was intentional; the logic being that data stored in file geodatabases is not meant to be multiuser.
That's fair. However, that completely ignores the use case of a single user making project templates for their own personal use. I certainly don't need a new copy of my DEMs every time I open a new project.
Currently, the workaround is to save map files and layout files and then just pull them in to the project.
What I'd prefer is a toggle during the APTX creation to just preserve references to the data.