I'm pretty sure that there was plenty of fuel margin. If it did come in too hot, there must have been some other reason.
My first thought is that the extra 'stuff' on the outside of the center booster required to connect the outside boosters might have caused some problems during re-entry.
That or simply timing issues. The center core should be faster than F9 is when it's coming in for landing, so if the compensation for that wasn't worked out quite right (possibly due to extra weight in addition to the velocity difference) that'd pretty quickly get it coming in too hot.
After all, it's only a few second difference between 'nominal' and 'way too hot' with the suicide-burn style landings.
Quite possibly, I just wanted to be generous. I'm not quite sure how much leeway the crush core in the legs plus 3-engine burn can offer. The 3-engine burn especially may give more options if they allow for it to be extended if the core is moving too fast, though it'd be understandable if that's not something they do.
My first thought is that the extra 'stuff' on the outside of the center booster required to connect the outside boosters might have caused some problems during re-entry.