It looks like there were a couple issues with the examples I originally posted above.

First, when I tried the 2nd example again today in a fresh repl, I realized it doesn't work as-is. After fixing it, I get the following error:

>>> from decimal import Decimal
>>> from pint import Quantity, UnitRegistry
>>> ureg = UnitRegistry(non_int_type=Decimal)
>>> d2 = Quantity(Decimal("1.0"), ureg.inch)
>>> d2.to(ureg.thou).magnitude
Traceback (most recent call last):
[...]
TypeError: unsupported operand type(s) for ** or pow(): 'float' and 'decimal.Decimal'
>>> 

I think when I was originally trying this out I had accidentally typed ureg = UnitRegistry() in the repl before running the d2 example:

>>> from decimal import Decimal
>>> from pint import UnitRegistry, Quantity
>>> ureg = UnitRegistry()
>>> d2 = Quantity(Decimal("1.0"), ureg.inch)
>>> d2.to(ureg.thou).magnitude
Decimal('1000.00')

The second issue is that I was importing Quantity directly from the pint module instead of from the UnitRegistry instance. If I change the d2 example to use ureg.Quantity then I get the same results as the d1 example:

>>> from decimal import Decimal
>>> from pint import UnitRegistry
>>> ureg = UnitRegistry(non_int_type=Decimal)
>>> d2 = ureg.Quantity(Decimal("1.0"), ureg.inch)
>>> d2.to(ureg.thou).magnitude
Decimal('999.9999999999999999999999996')

Couple questions:

1. Why does ureg.Quantity behave differently from from pint import Quantity?
2. I'm still confused as to why there is a loss of precision when using Decimal numbers in the last example. Is there a way to rewrite this so that the conversion does the equivalent of Decimal("1.0") * 1000, i.e. the conversion returns Decimal('1000.0')?