Personally I would write this inversed, saving some parenthesis and reads a lot easier:

if (!$container->hasDefinition('cache.annotations') && !$container->hasAlias('cache.annotations'))

Is it a preferred way in this project? From practice I can say that thinking in NOT (x OR y) is less confused than NOT x AND NOT y as first you could reason by simple positive predicate and then just negate it:
hasDefinitions := X OR Y; and negation would be: hasNotDefinition := NOT hasDefinition;

In second case it would be confusion as we immediately start thinking from negation hasNotDefinition := NOT x AND NOT y; and then positive would be: hasDefinition := NOT hasNotDefinition -> NOT (NOT x AND NOT y) (pretty complicated?) we need more transformations: (NOT NOT x) OR (NOT NOT y) -> x OR y;
Generally we use more positive logic in daily life than negative and it's easier to reason about.

Personally, I find it less confusing when an inversed condition is not a composed one. So I find@iltar's suggestion more readable.

The less parenthesis andOR present in a condition, the easier it is to understand. Especially in guard clauses you want it to be as specific as possible withAND:
if x AND y AND z; then return

Ok, changed to AND if it's better. But if it would be if x AND y then yes it's better, but now there is if NOT x AND NOT y and is more difficult to reason than if NOT (x OR y); In natural language the more negations is in the sentence the harder to know a real meaning. ( seehttp://www.grammar-monster.com/glossary/double_negative.htm )