Just went and read Air Trans Sporting Equipment policy. For bikes its an additional $79 (which would tend to support stacking the first checked bag fee, which still sucks)

And the requirement is in a box with no exposed parts, with no mention of any size restriction.

The policy for other various Sporting equipment is that standard overweight, and over sized charges apply.

Thus the clear negative implication is that oversized fees do not apply to bikes packed in standard boxes. (in other words if they did apply, they would say so, as they do for other sporting equipment, and the $79 fee is intended to be in lieu of such charges.)

The actual result you may get at the Airport is likely to depend however on the intellect and demeanor of the Gate Agent.