Hi,
As per the GST Act, if your aggregate turnover is more than the threshold, you are required to be registered. Here your aggregate turnover includes your turnover for any of your branches (as such branches are covered under the same PAN). Therefore, assuming that since you are registered in Gujarat you have an aggregate turnover of more than the threshold limit, you should be registered in Maharashtra as well.
However, if you're not registered in Maharashtra and are required to raise a tax invoice you will have to do the same through your Gujarat registration. Thus place of supply shall be Gujarat. However, in such scenario, you will not be able to raise an e-way bill from Maharashtra to Gujarat and you will still be in violation.