What
does it even mean to say that the universe was the size of an atom?
It may or may not mean anything.
Often such things are said without much regard to whether they
mean anything or not.
1) If the universe is closed, then it has a well-defined size.
2) If the universe is open, then the usual notion of size does
not apply.
3) There is however the notion of the size of the /visible/
universe, which has more to do with the age of the universe
than its intrinsic size. As you look farther out, you see
(a delayed image of) things when they were younger, until
eventually you run out of time.
This applies to open universes and sometimes (depending on
details) to closed universes.
a) Taking the earth as a model of a /small/ closed system,
this notion does not apply, since you can run an optical
fiber all the way around the earth and use it to look at
the back of your head. The earth is small compared to
its age, in the appropriate units.
b) In contrast, in some models of a closed universe, the
universe is closed but very large and expanding ... such
that you cannot see the back of your head. That is, in
such models, size exceeds age in the appropriate units.
Observations are limited by the age, not the size of the
universe.