Another uncomfortable fact: dissociating cells dramatically changes their patterns of gene expression, with immediate early genes turning on in minutes and a whole host more within ~half an hour of an exogenous stimulus (and chewing up tissue is a big one.)
Simple result in Nature shows flow doesn't just destroy spatial context but tosses out important biology. Activated T cells are usually physically stuck to tumor cells and gating pipelines toss them out. Up to 91% of T-cell/tumor clusters gone. A huge fraction of clinical IO papers that used single-cell flow on dissociated tumors have systematically deleted the most tumor-reactive cells and then drawn conclusions from what was left