The Transactions API in Orders does not provide any option for time-based filters, and works for only one Order at a time.
Is there a way to retrieve all payment transactions across all orders - after a certain timestamp? Without this feature we're having to query - 1 order at a time - for all orders in the past month or so - which is very time consuming and unreliable (there could be a refund on an order 2 months back)
Time-based filters are supported for most (other) APIs. There's a "Shopify Payments" API - but I believe that's only for those transactions for which Shopify Payments gateway has been used.
Or is there a way to do this via GraphQL?
There is not. If refund creation notifications are your focus here, you could look into subscribing to the refunds/create webhook.