I don’t see Security Suite Subpanel in SOME modules

The Security Groups Subpanel is not created by default for custom modules.

You have to create it manually in custom/Extension/YOUR_MODULE/Ext/Layoutdefs.
Create securitygroups_Layoutdefs.php in that folder (the file name is not significant) with the following contents:

<?php
$layout_defs['YOUR_MODULE']['subpanel_setup']['securitygroups'] = array(
	'top_buttons' => array(array('widget_class' => 'SubPanelTopSelectButton', 'popup_module' => 'SecurityGroups', 'mode' => 'MultiSelect'),),
	'order' => 100,
	'sort_by' => 'name',
	'sort_order' => 'asc',
	'module' => 'SecurityGroups',
	'refresh_page'=>1,
	'subpanel_name' => 'default',
	'get_subpanel_data' => 'SecurityGroups',
	'add_subpanel_data' => 'securitygroup_id',
	'title_key' => 'LBL_SECURITYGROUPS_SUBPANEL_TITLE',
);

You would also need to define the label for LBL_SECURITYGROUPS_SUBPANEL_TITLE in your custom module language file.

Then run Repair / Quick Repair

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