In my tests with a six lead 12 V, 50 ohm/phase motor using full step operation, it did not seem to make a difference if I connected the two center taps together, converting it into a five lead motor. The motor worked normally, even under load. Indeed I used an oscilloscope to look at the voltage difference between the two center taps and although there were some switching transients, they were small and probably would not affect the performance. I next tried out a small five lead motor and observed normal behavior (once I figured out how to connect it). So at least for full stepping, there appears to be no problem using the A4988 with some five lead motors.
However, I did not experiment with either the current limiting or the microstepping feature of the A4988, so I reserved judgement.
When you think it through, during normal full step, full current operation, the center taps should be almost always at roughly ground potential due to voltage drops and that is what I saw with the oscilloscope. If five lead motors work in your case, go ahead and use them!
Perhaps the Pololu engineers could look at this issue more thoroughly, with a variety of motors and driver options, and come up with some guidelines based on experimental data. There are lots of cheap, surplus five lead steppers that are perhaps unfairly being marginalized!