If I understand you well, users at your sites will use external link syntax to point to internal page ? Well if you can't educate your users, you can still write an action plugin that catches the IO_WIKIPAGE_WRITE event. In your handler, you have access to the page wiki text, and you have the possibility to change that text before it is written. See
https://www.dokuwiki.org/devel:event:io_wikipage_write. A global search and replace could change external links that point to an internal page into a real internal link.
Now the second problem: make external links that match *.myfunkywikis.com internal links. I think you can write your own renderer plugin to extend the
Doku_Renderer_xhtml class.
See the
documentation on renderer.
In your class, I think you only have to redefine 2 functions :
interwikilink and
externallink.
In the function externallink(), if the link matches *.myfunkywikis.com, render it as an internal link. The same for interwikilink().
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The plugin wizard will create the plugin structure for you.
https://pluginwiz.dokuwiki.org/