I only see Elite tokens as end of event rewards only. I have not seen them in any way replace standard tokens during the event. I am at clearance level 7 and Deadpool’s event has given me several standard tokens so far. Maybe this is as intended and they just misspoke?
This is a quote from the announcement regarding Elite Tokens.
"Starting with S.H.I.E.L.D. Clearance Levels, there will be a new token that players can earn: Elite Tokens.
The contents of Elite tokens consist mainly of 2-Stars (76%) with 3-Stars being a rarer reward (24%). Elite tokens will replace Standard tokens starting in S.H.I.E.L.D. Clearance Level 5 (Rank 20+) to help players transitioning from 2-Star to 3-Star rosters."