After upgrading the SEP Manager to 14.3 RU5 from a previous version, Custom Client Install Feature Sets have all components enabled regardless of previous settings.
Feature Sets with Endpoint Thread Defense for AD and Web and Cloud Access Protection disabled now show as enabled.
14.3 RU5 using custom Client Install Feature Sets
Changes to the Feature Set Version groups for Client Install Feature Sets in RU5 caused custom settings to be overwritten with default Full Protection values.
Feature Sets are now grouped to include the new 14.3 RU4 and later category, and the addition of this category caused custom settings to be overwritten.
This issue is resolved in 14.3 RU6.
A workaround is also available if upgrading is not an option at this time. Follow the document below to create an Install Feature Set that doesn't have the Endpoint Threat Defense for AD and Web and Cloud Protection features checked. Then apply an Install Package to the desired groups with the aforementioned Install Feature Set selected.
Add or remove features to existing Endpoint Protection clients
https://knowledge.broadcom.com/external/article/177413/add-or-remove-features-to-existing-endpo.html