Hi
The basic idea here is that the rule update changes the default policies. Be it balance security and connectivity or connectivity and security and so on.
Cisco release rule updates with revisions of most common signatures which should always be in drop and generate and some in generate events while also some rules without any action depending upon the base policy.
If you are using balance security and connectivity, that would be most safe (and recommended) base policy. To answer your question, no rule update installation does apply on base policy which affects custom policy as well.
Hope it helps,
Yogesh