url_fordoes not support your use case, but if you use it inside the Jinja template, you can simply add a call replaceto remove the encoding:
{{ url_for('get_user', user_id='%') | replace('%25', '%') }}
Alternatively, if you pass the URL in plain Python code, you can use urllib.parse.unquote(or urllib.unquoteif you are still in Python 2):
url = url_for('get_user', 'user_id'='%')
url = unquote(url)
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