This will be easily done by adding a config variable $wgShowDefaultBanner and adding a check for it where default banner is added. I'll add a patch this week.

Change 224089 had a related patch set uploaded (by Sumit):
WikidataPageBanner prefix class names with wpb-

https://gerrit.wikimedia.org/r/224089

It seems that migration is easier than thought, a simple modification of http://en.wikivoyage.org/wiki/Template:Pagebanner, to add a call to {{PAGEBANNER}} inside would do the trick. Since Template:Pagebanner is already used on English wikivoyage's pages, no modification of individual pages may be needed. See this example template http://pagebanner.wmflabs.org/wiki/Template:Pagebanner which uses the extension to render a banner on http://pagebanner.wmflabs.org/wiki/Canada

Change 224089 merged by jenkins-bot:
WikidataPageBanner prefix class names with wpb-

https://gerrit.wikimedia.org/r/224089

This will happen after deployment.

Deployment is done. Who's planning on doing this part?

@kaldari, testing of banners from wikidata still needs to be done, on a few select pages, after which the decision to migrate all pages to use the extension would be taken by the community. See T108839