Why are AMP pages "Excluded" in Google Search Console

AMP pages will always show up under the "Alternate page with proper canonical tag" list. This does not affect their being indexed and this message is expected. 

We do not replace your Shopify pages with AMP pages but have them alongside or parallel to your Shopify pages. AMP pages are an alternate but faster version of that page. Each AMP page contains meta-data that points to the non-AMP version of the page (the canonical page).  Google correctly identifies these pages as being an Alternate page with the proper canonical tag. However unlike other pages, it treats AMP pages differently and does index these pages.

AMP pages simply use a special kind of indexing which is only for AMP pages, so Google doesn't show them as directly indexed.  Instead, they are "Excluded" but the ones that are indexed will show up in the "AMP" tab in Google Search Console.  Again, having AMP pages show up as "Alternate page with proper canonical tag" is intentional by Google, and does not affect their indexability. You can check this from mobile when you search for your pages and find the AMP links. 

Here is some more information from the Google Support forums regarding this: https://support.google.com/webmasters/thread/166359031/amp-alternate-page-with-proper-canonical-tag?hl=en