Well, it's exactly the opposite actually. Percent value works much better for environments with varying datastore size due to its dynamic nature (larger datastores tend to have more and larger VMs, which will consume free space much faster during backup). Using percent value was driven by the customer feedback and VMware best practices, and based on multiple "production down" situations we have been observing in support in the past years due to using the absolute warning amount.
Remember that VMware explicitly recommends keeping 10% of datastore capacity available to accommodate VM snapshots (instead of recommending some absolute amount regardless of datastore size). In fact, this recommendation is exactly where the default 10% warning-threshold comes from.
That said, the absolute stop-threshold value is still available as before, using the same old registry key (see What's New in 9.5 for details). You can use this to protect those tiny datastores from overfilling if you choose to set your warning-threshold % to a very low value.