I think I figured out what is going on with the DMA write corruption. At least for the most part.
The HC CPU in the STE works fine as normal. However in this particular machine when the booster is added, even when running at 8MHz, it causes write failures on the hard drive.
Basically when copying my test floppy to the C: drive, it would intermittently lock up with " data on the drive may be damaged" . This is the hard drive not the floppy drive! It would consistently do this pretty much exactly the same files every time. There was also odd read problems as well in the mix.
I remember having no end of trouble with the clocks on the STE in early booster work. In that when the original CPU is in there, it just loads the clock slightly different enough for things to work properly.
The STE I am testing is the one with the internal blitter with a -38 DMA. I also remember
documenting the clocks with different amounts of noise on it between the internal and external blitters. This resulted in lots of weird and wonderful mods originally on the STE boosters clock depending on motherboard revision. Looking back it seems the external blitter and more problematic with the clock than the internal blitter motherboards.
So the clock on the DMA is basically this..

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8.5V P-P! No wonder the poor DMA is unhappy!
So I did some hackery to add a 100R resistor in series with the DMA clock line..

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And now the hard drive is a lot more stable and there does not appear to be any more write issues.
So while the HC CPU tends to solve one set of DMA related problems, it is perfectly possible it could actually create problems on the DMA. However this is not limited to simply swapping to the HC CPU either. it just as a more dramatic effect as opposed to changing between brands of NMOS CPU.. which is also generally enough to make or break "DMA problems".