My guesses:
1: I always get UPS, but maybe shippers like UPS set the prices in each country in Europe? If it's by truck, maybe the number of borders they need to cross? France 1 Spain, 2.
2. Protectionist action by each member state.
In any case, anger won't help. Thomann try to be the lowest price anywhere. I know they annoy all French music stores because the stores here can't match their prices. When I bought the YDS, I wanted to get it here so I told the store they had to match Thomann's price for me to buy it. I figured it was not only good to support them, but for returning it or service, I wouldn't have to ship it back. The 50€ free shipping is a pretty sweet deal because two Légère reeds or a 15-20 reeds will be shipped free to me. Or 18 Vandoren Blues Alto reeds 2,59 each, shipped free. They're a little over 3 in the store, IIRC. Just looking now at Amazon FR, the Légère American Cut are 3€ more than Thomann. That's significant!
I think you have the UPS thing right....they have their own policies on prices whereas by postal service Thomann just tacks on whatever extra they want for "service".
As to the reason for not having a set price for all the EU countries as one, that has always made it clear that the EU is still just an amalgam of separate independent countries rather than a unified super-state, in the sense of the USA. There postage depends on size and weight for many classes of mail rather than the distance it has to travel calculated by zones. They also have flat-rate shipping for types of shipping that would normally cost more because of the distance the parcel is being sent. None of that idea has been put into practice in the EU, and it seems to me to be a road block to small companies being able to do business outside their own borders as well as private individuals being able to buy from other EU countries online.
The other fact is that even when the UK was in the EU, being able to retain the pound as opposed to going to the Euro like almost everyone else, was a big deterrent to EU residents against shopping there. Actually, until the USPS raised their rates so high, and the Spanish Gov revamped the Customs service to snag everything and jack us up like highway robbers did, buying from the USA was always a lot cheaper than from the UK, given the much lower exchange rate of the former compared to that of the latter. Now that is a moot point since the UK is totally out of contention as a place to shop. Doing so is now a double whammy, hitting us for the higher value of the pound and for the duty we now have to pay for shopping there. My opinion is that they are going to be regretting this very soon, if they aren't already since who needs them now if their goods are overvalued and also too expensive to import? It's going to be a case of tough titty, but we told you so way in advance.
To prove that one only needs to look at the current exchange rates for the euro to both the dollar and the pound on a site like x-rates.com/calculator. I use it to calculate the relative values of sax stuff on the various eBuy sites to see how the prices compare in Euros and weigh that against the relative costs of shipping and duties, if any.
Right now there is a difference between the dollar on the lower end and the pound on the higher of 31€ per 100. That ain't just spit when we're talking about a saxophone that costs several hundred quid compared to fewer dollars, given that all American horns cost more in the EU and UK already. Looking at the various eBoy sites in the EU countries the prices for American horns is totally outrageous in Germany, Scandinavia and the NL.
For example, there's a Martin Comm III from Germany going for 2.400 euros, and it's a terrible relac not worth more than $1,400 in the USA or even in Spain. Then there is a reelaced Martin Imperial going for 1,500 euros when those student horns aren't worth more than $600 in good original shape. Worse yet is an Indiana in miserable condition that some shop in Germany wants close to 1,250 euros for!! The seller is either demented or just an out-and-out crook because I knew a guy who sold an Indiana in better shape than that for $250 on SOTW simply because he needed cash desperately and as was typical of the nickle and dime members back then, he had to keep lowering the price while everyone sat on their hands not buying it at the reasonable price he had it for. They knew the poor guy was hard up and needed the cash to get his car fixed, so he could get to work or school or whatever it was, but they just let him sweat it out and practically give it away. And these were people who pretended to be his friends when the subject was something else. That right there was one of the things I most disliked about that forum and many of its members who let no opportunity go by to cheat someone out of a fair sale or to screw it for them by making negative comments about that particular model of sax or mouthpiece even though they were not in fact interested in buying it.