The SCSI controller on the A4060DT isn't 'rubbish', it's the same NCR 53c710 chip as the Warp Engine, it's the quirks of the driver for it that's the issue (ie. will only automount and boot FFS formatted partitions, limited to 4GB partitions max without NSDPatch, etc.).
I've managed to get it to create, format and recognize a 30GB partition with OS3.9 and the right NSDPatch line on SCSI which appeared to function, though I hear there may be a possibility data written over the 4GB barrier may get corrupted depending on how the driver was written.
In terms of speedup over a 68040/40MHz CPU a 68060/50MHz will give you a 2-3x speedup, depending on the task. The memory on the A4060DT supports memory interleaving for better performance, though the board can be very picky about what RAM sticks it will work with when this mode is enabled. When I had a A4060DT I managed to find some RAM that would work with interleaving mode and found it gave around twice the memory speed than with it disabled.
I would recommend the A4060DT as an upgrade from the Warp Engine if you can live with the SCSI driver limitations and manage to find RAM that works with interleaving mode. The board is a well built piece of hardware. It also tolerates a certain level of overclocking of the CPU as well.