Global configuration item not always being used

[wlymanambry]

Describe the bug
I set a global_config setting like:

global_config.normalizer.shuffle_direction = 5

I then call assembly_mapper:
variant_mapper: assemblymapper.AssemblyMapper = assemblymapper.AssemblyMapper(
connection,
assembly_name="GRCh37",
alt_aln_method="splign",
normalize=1,
prevalidation_level="INTRINSIC",
)

with a print statement, I can see that this config value is set correctly here in assembly mapper:

But when the Normalizer class is initialized, it is pulling whatever value is in the _data/defaults.ini file (and I'm not sure why)

A print here shows this is '3' instead of the expected 5 value that was set:

To Reproduce
Described above

Expected behavior
For this configuration value to be set globally