The pattern in what you liked and what you didn't is worth naming, because it predicts the rest of the market. Abicyclette is a small French outfit that draws its own routes. Radweg-Reisen and the Danish operation are volume businesses, and a volume business routes you down the national cycle trunk route because it is the only line it can guarantee to a thousand people a season. Vienna to Budapest is the extreme case: the Danube path is effectively a cycling motorway with a hotel every forty kilometres, and it gets sold precisely because it never goes wrong.
So the filter is not the country, it is the size of the operator and who owns the routing. Three questions sort it out fast.
Ask who drew the GPX. If the answer is that it follows the EuroVelo or the national route, you will get the trunk line. If they can tell you why they leave it at a particular point and where they rejoin it, somebody has actually ridden it.
Ask for the hotel list by name before you book, not by category. "Three star, centrally located" is how a volume operator describes whatever bed it managed to contract. A small operator names the places, because the names are the reason it charges more than the others.
Send one genuinely awkward question at the enquiry stage - an odd bike size, a request to add a night in the middle of the route - and time the reply. That single test would have told you about both of the ones you disliked, before you paid.
On where to look: for boutique hotels with routing that is not the trunk line, the small national operators generally beat the big German and Austrian ones. In Italy, Slovenia, Portugal and rural France there are one and two person outfits doing exactly what you describe. The problem is that they market badly in English, so they are close to invisible from the UK. There are marketplaces that pull them together - I should say I am involved with one, so weigh that however you like - but the three questions above work whichever route you go in by.
One practical thing. If you want boutique hotels and a route off the main line, book earlier than you are used to. Those places have ten rooms rather than eighty, and the shoulder season weeks are the first to go.