The numbers aren't the same because there are more cells in the tuneboy fuel trim table (640 vs 234 in the PCIII map) so they are averaged. If the cells in PCIII go from 36 to 30, then in Tuneboy they go 36, 34, 32, 30. That is why they are different.
The example given is confusing. Is that the same bike on the same dyno? One run with PCIII connected then subsequent run with it disconnected and PCIII imported into Tuneboy. I have done just that and have not experienced a noticeable difference. Did the bike have an O2 bypass on or just have it turned off via Tuneboy with O2 sensor still in place?
Also emulating a PCIII in Tuneboy is different than importing a .djm fuel map into Tuneboy.
I would say email Tuneboy for further info, but that would likely go unanswered.