Fixing up these ambiguities is exactly one of the things we make sure we do here. To do so, the rules must be consistent and clear, so we know which ruling is correct.
So here's how I think these contradictions between cards and rules should be handled:
For every rule, it either is or is not an "Absolute" rule. (Ellesar's Armpits will find this very familar)
An "Absolute" rule is one that cannot be overruled. Specific rules can be identified as "Absolute", the rest are not. The thing that needs to be done is to identify the "Absolute" rules, and clearly identify them upfront in the Rulebook. Here are the ones that I think are "Absolute":
1) "Absolute" rules cannot be overruled.
2) Whenever a card's game text contradicts a non-"Absolute" rule, the card takes precedence.
3) Whenever a card's game text contradicts another card's game text, the "not" situation takes precedence.
4) Erratum for a card replaces what is on the printed version of the card.
5) The Rule of 4.
6) The Rule of 9.
All other rules have the potential to be overruled by a card's game text, even though most rules don't have a card that overrules them.
So to determine some of these issues, we need to determine whether a specific rule is "Absolute".
For example:
1) Is "You cannot play an event during a phase that does not match its phase action." an "Absolute" rule?
--
Diversion,
Bilbo, Bearer of Things Burgled with
NFFATROD,
Pass of Caradhras with
Caradhras Has Not Forgiven Us.
2) Is "Each character may bear one possession or artifact of each class at one time." an "Absolute" rule?
--
Flaming Brand,
Hand Axe, etc.