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Hello.
Does this mean that access from SUBNET A is NATed on INSTANCE A and then sent to Transit Gateway?
Also, as part of troubleshooting, please use something like Network Access Analyzer to check if you can communicate with Transit Gateway.
https://aws.amazon.com/jp/blogs/aws/new-amazon-vpc-network-access-analyzer/

The idea is not NATing traffic on instance, but leave it as it is coming with its original IPs. Only that it requires allowing it to go through this intermidiate router.
For example, have you confirmed that communication is possible from SUBNET A to SUBNET B ENI? Also, if you are not using NAT, I feel like you probably need to add a route back to SUBNET A in the route table to SUBNET B's route table and TRANSIT GATEWAY and INSTANCE B's route tables.