I find them extremely useful. Something like Melda Auto-Align is what I use. Yes, if you are just aligning two recorded tracks, waveform works fine. However, the issue happens when aligning multiple parallel tracks post-processing. For example, I tend to duplicate a bass track three times and process them separately (DI, AMP, Distort). Since these are the same source signal, the waveforms would technically line up, but the processing changes this drastically, so using a phase alignment plug-in makes a huge difference in the tone. I was surprised the first time I heard it, but now it is something I use nearly every mix.