Agreed there were issues on the X4 and I'm glad that the council sorted these in Naptan. It may be worth you trying
Elydiums Naptan viewer which has a full map showing all of the stops in Naptan, both active and inactive. This may help you going forward to find stops which aren't present on google maps. In relation to this and your KPMG comments, I agree there are external issues and where this is the case, I don't make any criticisms of the operator as it's things not within their control.
I had seen the NuVenture experiment thing that was done and publicised by
Busandtrainuser, it was quite informative. It is rather interesting how the GPS drifts so much depending on who is consuming the data. Worth noting though for the purposes of clarity, I acknowledge and appreciate the fact that GPS drift doesn't seem to be within operators control and so I haven't made any criticisms against the operator for this issue.
Some AVL issues are within the operators control though such as not adding a route to their AVL feed and so I can make comments on that.
Even without BODS, you should be adding all of the stops into Ticketer for new routes and adding all of the times, because that is what would be required for revenue protection or data collection purposes. Any incorrect data, irrespective of BODS would have a negative impact on the company as well as contractors (local authorities or schools) who the company works on behalf of. It's also worth noting that incorrect data in the Ticketer portal also affects drivers because their machine stop lists will be incorrect.
If it was one or two things it wouldn't be so bad, but every single normal service route on Connexions open data is either missing stops, or claiming to serve stops that aren't served, or stops are in the wrong order. For example, route 21 towards Halton you have the buses going the wrong way around Colton loop. That won't bode well for any statistics as you aren't serving stops in the right order, or operating the route that your own timetable data claims the route goes. On route 21 towards Halton alone, you have 12 stops missing, and 10 stops in the data which you don't serve. That's one single route.
And if you are going to bring up about on time performance stats from BODS, it's worth noting that the better your timetable data is, the better your on time performance figures will be on BODS. While yes there are things that you can't help (GPS drift), you can help your timetable data.
For clarity and balance, many companies comply with bus open data, including but not limited to those using Ticketer for their open data needs. I fully acknowledge and appreciate there are some things not within an operators control and it would of course be unwise of me to criticise on those those things. Criticisms I have are where issues are within an operators control, and even then that is only when operators who have a large number of issues (ie Connexions where almost every (if not all) routes in the BODS dataset are missing stops, linking to stops on the wrong side of the road or simply stops which aren't served, stops in the wrong order or various other 'basic' issues).