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appears the problem is with small halos only. larger ones are aligned correctly. So, the fix in c6e5639 mitigates this issue because in general cairo halos were being drawn to small.
as for the underlying problem, not sure what it is, but it may be on the cairo side. Closing this as I don't see value in much further research at this point. Anyone reading this - please open a new ticket if you feel like cairo halos are still to shifted to look good in your maps.
It may be that #1290 would be a good workaround.