Yes Jean was always an Omega...Jean and Bobby were designated as such as teenagers, well before even beginning to realize their potential.
And Sentinel "Omega" designations or those from other realities or timelines do not automatically carry the same meaning as what has been used over the last 20 years in 616 (unlimited potential/undefinable upper limit)...Greek letter rankings are pretty generic and can be used to denote current power, potential power, threat/danger level, priority for capture, political/influence, etc...in fact the Sentinels themselves are ranked in Greek letters based on their model capabilities. You can't just unilaterally take any utterance of "Omega" and think it has the exact same connotation as what is being used now