Thanks for the Comment Jithin.
Based on the Repro from our environment, We had chance to choose only among 4 Tiers for the Application gateway Ingress Controller.
Tried with Standard V2 and we do not have options to increase the Backend HTTP Settings more than Maximum 100 limit.
Tiers Available:

Possible Solution:
When creating the 1)AGW IC we would add both servers to the backend address pool 2) Create a probe for each subdomain 3) Create a backendhttpsetting with each probe? Or create with no probe?
Other Option:
You can achieve this with multiple http settings, each with its own probe. For example if you have a.domain.com and b.domain.com running on the same set of backend servers, you would create two http settings and two custom probes. Probe1 would probe on a.domain.com as host name and probe2 with b.domain.com. Your backend pool will be a single backend pool with the two servers. Now you can create two rules and attach the two probes & settings to the rules and point them to the same backend pool. The probe will only mark down a.domain.com or b.domain.com but not the whole VM. Hope that helps.
Reference SO Thread: Azure Application Gateway Probe Configuration