Followed your suggestion and asked Jeff at FD. Seems its best to disable the DBW when setting the PIS. Inserting the plug into the harness will do it. I also asked about disconnecting when having the car serviced. I have pasted Jeffs response.
We do recommend that you bypass the DBW while setting the PIS, the main idea there is that the tech should set PIS, drive the car, try another value, drive the car, etc until he feels that it's in the best position. If the DBW is installed, we find that many shops (that aren't very familiar with the product) will tend to spend less time and effort to dial it into the best position since it already feels better than most cars they are used to.
If you bring the car to the dealer, we also recommend bypassing it. Just in case the dealer finds any problems all their diagnostics will report correctly also.
If you're in for an independent service and are out of warranty, you may not bother to bypass it. Technically, it's not required.