Very interesting read. Having ventured a few times to the continent (but no flying, we are ferry enthusiasts) I agree with much of what you have written. A few points :
"I've visited the North Netherlands a few times and it's a gem! quiet rural lanes wide open skies and, a more relaxed way of life. Only problem is getting there! There are no flights or ferries from the UK so you have to start in Germany." 100% agree with the "gem" description, generally we really loved north and east Netherlands. There is though a flight from the UK - Flybe have a Southend to Groenigen route (no idea whether it is bike friendly as maybe it is a very small plane)
Having ridden from HvH to Berlin last year I don't 100% agree with your comments on German cycle routes and drivers. In 500 miles I think we only once encountered a driver who was aggressive to us (probably when we weren't using a cycle track, although 99% of his fellows had no problem). Generally I would rate the German drivers top of all the countries we have visited for politeness and consideration - many hang well back very patiently to make a safe overtake. We plotted a route with a mix of cycle routes and main(ish) roads - and were happy to cycle on roads with no tracks, but equally found many roads had adequate tracks and some had very nice new ones, so probably an evolving and improving situation. I agree about tracks through villages, but we watched what the locals did and just went onto the road, although there were sometimes some fiddly crossing back and forth issues.
+1 for Stayokay hostels - although be aware that most (all?) don't have self catering kitchens, but they do have nice bars. We used German hostels last year which were more traditional, and usually full of school children (at least in Sept), but we were made very welcome and there was undercover bike accommodation everywhere. As with Stayokays, breakfast included, but evening meals too early if doing long days.
It would be so good to be able to put Harwich-Esbjerg back on the list. We managed to get a trip the last year it ran (thanks to a tip off on YACF!).