I'm not saying that Felix didn't intentionally deploy his chute early to preserve that last record but here are a few points to consider:

Right before Felix deployed his chute he complained that he had poor visibility because his visor had fogged up. He had been having trouble with the heating element on his visor before the he made the jump as well. So it is possible he made the decision to deploy for safety reasons if he wasn't able to accurately gauge his altitude due to poor visibility.

Lastly, in the Project Excelsior jump Kittinger used a drogue to slow and stabilize his descent. This is at odds with what Felix was trying to accomplish which was to break the sound barrier and achieve the fastest free fall record. So, the difference in speeds between Kittinger and Felix may have been enough to prevent Felix from also beating the longest free fall record.