Are these BLDC waveforms making any sense?
Yes, the plots are making sense, but your imposed PWM is not 'in phase' with the BEMF voltage.

As you stated, you are driving this open loop, which is much more like a stepper motor, so your 'positive' will not line up with the BEMF positive.  When you start using your sensor feedback, then your BEMF will look much more like the example.

Keep in mind that the linearity of the BEMF is strongly dependent on the motor.  Don't be alarmed to see some curvature:



Notice that this waveform is 'in phase', meaning that the drive is applying a high to this phase as the phase is peaking.  That is what you want.  Right now, you are applying it at a different time, so you are out of phase.