From my understanding of the question, the author wants to know if we can save a site template containing it's subsites.
There are many workarounds (backup, export, individual templates), and I believe Tom has layed down some very good approach(es).
However, site templates are saved independently for each site (web), and not even PowerShell can overcome that, hence, my different answer.
As usual, some references:
Move root site collection
Anyway, I won't feel terribly disappointed if this answer is not selected.