So this a bit of an issue here. IABot is global, and this is a unique problem on enwiki. It's not a simple code change as any change has global implications.

So perhaps the solution is to abandon edits when |title= would contain a template because, who knows what gibberish templates emit when rendered. In mainspace at en.wiki, {{it icon}} produces this: <span class="languageicon">(in Italian)</span>[[Category:Articles with Italian-language external links]]. Any of the many language wikis that use a relatively recent version of [[Module:Citation/CS1]] will show the URL–wikilink conflict error message when |title= holds a template that produces a wikilink and when |url= has a value (as it will if the bot is creating a cs1|2 template).

At en.wiki there are any number of templates that produce wikilinks of some form or another. I would be very very surprised to learn that en.wiki is the only wiki to do this.