That Home Depot manager is wrong. If a safety toe boot’s toe crushes and damages your toes, you would have lost them in a soft toe boot too. It takes a lot of weight to deform an ANSI rated steel toe, or aluminum toe, and/or crack a comp toe, that would have Flat Stanleyed your phalanges in a soft toe boot. I’m not a crazy lover of industrial safety standards, but the idea of a good safety toe doing more harm than good is false.
Just like the people who will tell you that sometimes wearing a seatbelt is more dangerous than not. Being ejected and/or being partially ejected and then being crushed is almost certainly worse than staying in a car.
Gore-Tex is useful when it’s cold & wet. That’s why my Frank’s & White’s go on the shelf and I switch to Danner Quarry boots in the winter. I don’t really need an insulated boot, or a muck boot, but an all leather boot doesn’t dry in January like it does in June. That, unlike the safety toe, though, is just my opinion, and your experience may differ.