Using the Panopoly and Commerce Kickstart distributions together
I would do #2.  To my knowledge, all of the modules in Commerce Kickstart can be downloaded separately; Commerce Kickstart just offers some default configurations.  If you run into trouble setting up the Commerce modules, you can always install a copy of Commerce Kickstart on a local machine/another server and reference that while you are setting up your main site.

By contrast, the problem with #1 is that not all of Panoply is easily configurable if you are not using that distribution (for example, the responsive layouts).  So it will be much easier to use that, especially if you are going to host it on Pantheon, which is behind Panoply.

You could edit the distribution makefile but that is probably more trouble than it's worth; the Commerce modules are designed to be installed on any Drupal site, so adding them to Panoply is very straightforward.