This is not a regression. It is just an old bug. The --scrubWikitext option strips the whitespace to avoid adding a <nowiki> </nowiki>. So, the "bug" is in the nowiki-prevention code. Looks like presence of templates is what causes that because the nowiki code doesn't look inside the template to know that the leading whitespace is harmless for other reasons (ex: <div> tag on the line). We are probably not going to fix that since it does not seem worth the complexity for an occasional harmless dirty diff.
The selser patch I pushed recently doesn't prevent this dirty diff either since it looks for separator-runs between nodes but probably needs a special case for the very first non-separator-node of <body>. So, that is probably a better place to tweak this.