Bingo. I was going to suggest just about the same thing. I'd go with the Dan John/Dan Gable idea of "if it's important, do it a bunch." Make Zerchers 2x5 with a easy-ish weight the last part of your warm-up every training day.
If the bar placement bothers you, try picking up a pair of bar pads usually used for squats. Those work alright for some cushioning.
I will say, though, that Zerchers are like using the hook grip. It's definitely going to be uncomfortable at first. And for most people, I just don't think it's very necessary. If you're a strongman competitor or even a competitive powerlifter, sure, they have their benefit and carryover.
But for the average guy going to the gym, in terms of risk:reward (but "risk" is the wrong word), it just doesn't pan out. I'll occasionally do some Zercher walks, or do some sandbag stuff in the Zercher position (especially lunges), but not much in terms of barbell squats or good mornings.
With all that said now, I have a buddy who competes in the Highland Games and Zerchers are a staple for him. He actually begins most lower body days with a front squat/Zercher squat superset-type of exercise. Front squats with a weight, and then when fatigue sets in, he lets the bar drop down into Zercher position to bang out a few more reps.