Valid concern. Yes, there is a possibility of eNACH processing the full due in certain situations.
I don't use eNACH regularly. I keep it as a backup. So, no idea how each bank processes a payment done one day prior to due date. Even within the same bank (for example Axis that is known to process the payment almost immediately even before BBPS), due to technical reasons, a bank could delay the settlement resulting in eNACH being triggered for the entire amount.
In situations like OP who made the partial payment two days after the bill generation, there was plenty of time (more than 10 days) for settlement. If he/she had used eNACH, it could have triggered correctly for the pending amount.