Manish, the MIAB community is very active and this is what I like about MIAB 
Yes, its possible to run MIAB on sub domains. However, you have to use your registrar’s DNS as I did. Let me illustrate using the domain name, DEEET.COM, which is registered with NAMECHEAP and hosted on NAMECHEAP’s BasicDNS.
Now, I will create a sub domain, WORKERS.DEEET.COM, which is hosted on NS1.BOX.WORKERS.DEEET.COM and NS2.BOX.WORKERS.DEEET.COM. The IPv4 number points to a VPS on LightNode.com.
Now, I will create another sub domain, CUSTOMERS.DEEET.COM, which is hosted on NS1.BOX.CUSTOMERS.DEEET.COM and NS2.CUSTOMERS.DEEET.COM. The IPv4 number points to a VPS on https://vpsmalaysia.com.my.
So, now I have two domains hosted on two different VPS providers both running two different MIAB instances.
My registrar Namecheap hosts the main DNS for the domain name DEEET.COM, while I delegate DNS to the name servers run by MIAB Instances.
I hope you understand but if you aren’t clear, please tell me and I will gladly re-explain.
Have a nice day