Similar to other region, unfortunately it is the default setting/policy to have a QBO account for a single tax id, including on QBO India version.
You may have 3 options:
1. Open a separate QBO account for each tax id and utilize a 3rd party consolidating app.
2. Open a separate QBO account for each tax id and export the report to XLS for format to be consolidated manually.
3. Switch to QB Desktop with a single license to manage multiple company files.
You can create Tax code manually for your other GST registration in the same QBO account. For GST number to be printed in Invoice you can create a new Location and customise you invoice. You will not get GST report for the Tax code you add manually but you can get all inward outward details.
Let me know if any issues.
CA Alok Shah