docs: clarify that Session usually should be called - methods should not be used directly

Documentation based on clarification by Søren Løvborg:

Session is the factory/singleton manager, which tracks the current session (per
thread). To end the current session entirely and destroy the Session object, we
call remove on the manager (Session.remove()). (A new session will be created
on-demand.)

Session() returns the current session for the active thread (or creates a new
session, if there's none). commit is a method of the SQLAlchemy Session class,
thus called as Session().commit() ... it's a method call on the current Session
object, not the session factory/manager.

SQLAlchemy may have some hackery to allow Session.commit() to be called, and
the call automatically redirect to the actual Session object... but that's a
hack and should be avoided.

TL;DR: for remove, call it on Session; for everything else, call it on
Session().