Feature summary
I suggest to implement the "single line" mode in the Regular Expression mode. "Single line" means that the . matches newline as well.

Use case(s)
Since newline are ignored in wikitext syntax, it is very common to add newline to split parameters of complex templates in several lines. This improves readability by human users, nevertheless it hampers the possibility to quickly and massively make text replacements.

Benefits
It will make the extension more flexible.