You can't take two separate GST registration with a single rental agreement. You can divide the space in to two partition and enter in to two different rental agreements.
Yes, two gst registration can be obtained on the basis of one rent agreement. say for e. g. ABC Ltd rents a premises to PQR Ltd. PQR Ltd. wishes to share premises with XYZ Ltd. XYZ Ltd. can conduct its business at premises rented to PQR provided PQR Ltd. issues NOC to XYZ and further, ABC Ltd has not imposed restrictions of sub-lease.
I hope yours is the same situation. Pls feel free to let me know if my understanding is wrong