I am very surprised at your results...that the 2 ran hotter than the 3. I have not seen any complaints about overheating on the 2 on this or the Raspbian forums. That the uSD card was the hot spot was surprising as well...the same uSD for both? How big? You mentioned that it was hotter around the Raspberry logo...is it a small uSD card, 8 gig or so? Should not get that hot. Could be a bad uSD card. Try a 16G UHS1/class10 from San Disk. Are your charts vcgencmd results or from your IR thermometer?
As to your industrial setting concerns, I've been running a B+ for several years now, headless, 24/7 to control my solar water heater backup and no issues have surfaced (but the B+ runs very cool). The Broadcom chips are rated much higher than the 85C throttle point of the RPi firmware...105 or 125C IIRC so the headroom for the chips is really extreme. Even so, in that setting I would use a fan just to satisfy my paranoia.
As to tiox's comments, there are several cases on the market that incorporate and include a fan. For most people's use of the RPi, a fan is a needless source of energy drain and noise.