Changing the name of the flag is fine with me.

Having a warning for unescaped brackets that trigger set operations might also be a solution (once escaped they will still work on the old re).  Maybe the same could also be done for scoped flags.

FWIW I tried to come up with a simpler regex that makes some sense and triggers unwanted set operations and I didn't come up with anything except:
>>> regex.findall('[[(]foo[)]]', '[[foo] (foo)]')
['f', 'o', 'o', '(', 'f', 'o', 'o', ')']
>>> re.findall('[[(]foo[)]]', '[[foo] (foo)]')
['(foo)]']
(but this doesn't make too much sense).  Complex regex will still break though, so the issue needs to be addressed somehow.