This depends on how the document is written. The document will tell you if the match is based on the pay period (no true up) or plan year (true up) or some other method like quarterly, but that is more rare with our clients. If the document says the match is based on the plan year, then yes, you have to true up based on annual compensation and deferrals.
This statement is not adding up, maybe I am misunderstanding the way you use "safe harbor". But a 3% match does not qualify as a safe harbor match in terms of ADP/ACP safe harbor.