Because it is not a standard engine installation, there is no such thing as a "properly fitted" Holden engine installation. That said, ideally the angle of the gearbox should not change with the engine installation (should be horizontal relative to chassis datum), because changing it means the angle of the universal joints on each end of both drive shafts will no longer be equal, resulting in drive vibration and potentially rapid wear of the joints.
However, retaining this angle usually will mean that the front crankshaft pulley interferes with the front crossmember. Most conversions deal with this by modifying or moving the crossmember, but a few have dealt with it by raising the front of the engine just enough to clear the cross member, with all the problems you note. A very few, I suspect manage by moving the gearbox back slightly and generally using maximum manufacturing tolerances. Whether this is possible will depend on the actual flywheel housing adapter - they vary somewhat.
John
JDNSW
1986 110 County 3.9 diesel
1970 2a 109 2.25 petrol
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