Fix error code precedence to ensure disable overrides enable

The logic for resolving conflicts between 'enable_error_code' and
'disable_error_code' was inverted in two locations: Options.process_error_codes
and Options.apply_changes.

In the global configuration path, enabling incorrectly won precedence. In
the per-module override path, the logic allowed inherited enabling to
undo an explicit disabling.

This change swaps the set subtraction in process_error_codes and removes
the redundant discard operation in apply_changes to enforce the rule:
Disable always wins.

Fixes #20348.

Author: franzengel04