It is possible to use Cloudflare DNS for AMIMOTO managed sites after making a few changes to the default settings from the Cloudflare Dashboard.
It's important to disable their Proxy feature as Shifter provides CDN services through Amazon Web Services which it is built on.
Add ALIAS/ANAME record
1. Login https://dash.cloudflare.com/ and navigate DNS
2. Click [Add record] button
3. Disable Cloudflare Proxy
Click Orange Cloud ("DNS and HTTP Proxy (CDN)") and turn it to Grey Cloud ("DNS only") when adding records for bypassing Cloudflare on existing DNS records.
4. Add ALIAS/ANAME record
If you want to set ALIAS/CNAME record for Shifter on CloudFlare, choose CNAME from Type, input @ to Name, then click [Save] button.
Here is sample record.