I'm wondering if Pywikipedia messages like the one linked above("Bot: Redirect to a deleted or non-existent page") should be explicitely linking to Wikipedia pages, since Pywikipedia also has many users outside of Wikimedia. AFAIK, if one wants their custom reason, there is a --reason param to use.
That's not the problem. Thing is that the Pywikipedia bot is also quite in use outside Wikipedia, and thus pages like Wikipedia:Redirect or Wikipedia:CSD don't exist there. Links to such pages should be avoided in the message.