Hi Tim,
Since all of your store's HTML is rendered underneath Bouncer's popup, there are no known penalties that would harm your site's SEO.
I see that running PageSpeed on your site does produce some suggestions, but I can only find two minor ones related to the background image you selected on Bouncer. You can easily change the background image from your Dashboard if this concerns you.
Bouncer can be selectively disabled for any page. We have a helpdoc on this topic here: http://docs.theshoppad.com/article/90-can-i-control-where-bouncer-is-shown
Feel free to reach out to our awesome support folks directly if there's anything else we can help with: contact@theshoppad.com