All of the Implied Rules should be shown here.
See also: https://supportcenter.checkpoint.com/supportcenter/portal?eventSubmit_doGoviewsolutiondetails=&solut...
DNS has implied rules.
NTP is not covered under Implied Rules (at least the ones shown here).
However, if traffic were purely being accepted based on these implied rules, it would be accepted that way for both layers.
Which means...this "Implied Rule" is probably something different.
I'm assuming your Application layer only has App Control/URL Filtering active and not Firewall?
That might be the reason for the implied rule as DNS and NTP are handled in the Firewall, not App Control.