Have a gear box that appears to have had the diff tail changed on it at some time. There were no dowles between the gear box and diff tail housings.

When I fitted some dowles it was clear that the diff bearing bores were out of round, with a small step where the housing met – about 10 thou. The sides of the housings were pretty flat.

Is it acceptable to leave the dowles out, letting the diff bearings do the alignment?

Yes it is OK to leave the dowels out. But do check the roundness when bolted up.
It's OK to leave out the top and bottom gaskets if needed to achieve this. If you assemble without the gaskets use Loctite 515 or 518 or similar anaerobic sealant, it's designed for this purpose.

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DrMini- 1970 wasaMatic 1360, Mk1S crank, 86.6HP (ATW) =~125 @ crank, 45 Dellorto (38 chokes), RE282 sprint cam, 1.5 rockers, 11.0:1 C/R.