it's not that WinISD and BassBox are wrong, it is WE that are wrong for assuming that the results hold true for ANY port configuration. The numbers those programs spit out are generally for a free-terminating end (not using any enclosure walls for the port-walls).
Also, does reality and modeling agree if the port is round or doesnt share enclosure walls?
Absolutely. When you specify the correct end correction factor, a round or even square/rectangular port models very accurately,
so long as it is at least 1 equivalent-diameter away from any internal surfaces. It's once you get a circular port downright into the corner, or a square/rectangular port sharing one or more walls that requires modifying the length via the appropriate end-correction factor.
Horn Resp and Akabak lead to the same results. I believe they both use the lump-element model for the acoustic mass, so unless one personally accounts for the end correction factor from empirical data, slot ports like the ones in this discussion
will be tuned lower than calculated.
Modeling with free-ware like WinISD/HornResp/Akabak/etc/etc is not a problem. Just specify the Fb, and chuck off 30% of the calculated port length to get in the ballpark. If you want the actual seat # inside the ball park, then chuck off about 25%, then see what the tuning is at via the actual impedance plot and modify accordingly by progressively making it shorter and shorter. If you're old-school like me, you can use an end correction factor in the vent length formula k=2.227 that I found a couple years ago, and correlates nicely.