Currently testing 10.3.6 but looking at code this is still true in current 10.3.
Any setting of in_predicate_conversion_threshold in my.cnf is overridden in init_common_variables() with this line:
Removing this line appears to fix the problem. A default is set in sys_vars.cc anyway I don't think this is needed.
This affects ColumnStore because we need to set this high.
As a side note, I couldn't see this variable documented in KB.