OK. That's a defect in Manifold 8.
Two coordinate systems with equal parameters are considered to be the same even if the datums have different names and there is a custom conversion between them. There is no easy way to fix it, that's how Manifold 8 thinks about the coordinate systems - if all parameters are the same, then there is nothing to convert. Custom conversions between datums come later.
Here's what you can do: alter the major axis of the GDA2020 datum (its ellipsoid) by a tiny amount so that the results of conversions are altered by a proportionally small amount (chances are, they won't be altered at all because computation errors are higher), but the system would consider the datums - and thus coordinate systems based on these datums to be different.
Like this (the beginning of Australia Geocentric 2020 (GDA2020).xml):
<name>Australian Geocentric 2020 Ellipsoid</name>
I bolded the change. We added 1 nanometer to the major axis. That's right on the edge of the accuracy of a 64-bit floating-point value.
Hope this helps.