They are obvious if you have two copies and are actively looking for differences, otherwise not. If someone sent me a document with square brackets somewhere i wouldn't question their use of square brackets over parenthesis, unless they don't match.
There are many more options: Insert one of the many non-printing ASCII codes. Add an extra space, especially before a newline. Add or remove an extra newline at the bottom. Change punctuation where the choice is believable either way: Single quotes for double, commas for semicolons, periods for colons.
- replace quotation marks with two apostrophes
- replace “I” with “l”
- replace parentheses with slashes or square brackets
- replace commas with semicolons
Each of these substitutions can communicate a single bit while being ASCII-safe and likely won’t change word wrapping opposed to synonyms.