Yes, many CAD systems allow inherited nets or other invisible
connections. If you let this go unchecked it can surprise you.
And I've seen libraries where the 4th terminal is tied to a large
negative or positive voltage with some device params given
dummy values, the thinking being this would "kill" some features
that smart guys who never designed a circuit believed were
not relevant. Until you try to do low current analog and see
that KCL seems to be violated, and find out that even
dummied-out D-B and S-B diodes are conducting nanoamps
from "nowhere".
Now there is always a 4th terminal in a MOSFET. It may be
the substrate or it may be a little body pocket that comes and
goes with bias, or anything in between. A three terminal
approximation is just that, dependent on what you do to
make the body and source dead electrically equal. A BJT
in integrated circuit technology also likely has at least a 4th
terminal (outside of some SOI types where only a capacitor
connects collector and substrate). Most BJT models support
the 4th, ohmic (diode) terminal.
I'd bet that "sub" wants some realism applied. What this
means comes down to cases. Consider your technology's
cross-section construction and try to represent its likely
electrical attributes (potential, resistance between that
source and the devices and each other - a nasty little
mesh at anything above trivial complexity).