No it isn’t a different debate, the 2 are directly linked, without brexit, a second referendum would most likely not even be a debate because there would be no likelihood of it winning.Even a a proper deal with some sort Norway partnership with the eu would similarly make the independence debate irrelevant, the deal Johnson wants, even if he could get it isn’t wanted in Scotland along with his Irish borders and is what will break the UK apart.
When that happens Johnson his government and his supporters will be the ones that are to blame. No doubt though they will try and blame those that have never made any secret that they wanted independence.