About that lens choice
That XF 18-55mm f2.8-4 R OIS is a good choice as a first lens, even if you want to go full manual control. All fuji lenses with an R in the name have that aperture ring on the lens itself.
Also 18-55mm is a great range and since it's often sold as a kitlens you should be able to find it second hand for cheap (even cheaper than that 400 EUR you listed). After a good time of shooting you'll be able to filter your pictures and see what focal length you use the most. At that point you can pick one of the compact primes in that focal length to get a faster lens for cheap (used or new).
The only thing to watch out for with this lens is that the max aperture changes when you zoom in or out. Unless you use it on f4 all the time. Just something to be aware of, no real issue if you watch your settings anyway.
The XC series are cheaper lenses from fuji, like the XC 16-50mm f3.5-5.6 which is optically as great as the XF you already considered but made with more plastic and without aperture ring. If you can live without the aperture ring that is an option also. The XC 15-45mm I would stay away from, that one has a switch instead of a zoom ring and when in use extracts a lot right away so isn't as compact as it might look.
Although for landscapes you won't need a fast prime. You could still consider a prime for slightly sharper images. But again for landscapes you're stopping down that lens so you probably won't notice it. Might be a better option to go for the XF 55-200mm once you're ready for a new lens.
Another lens that might be on your radar for the future is something like the XF 10-24mm f4. I wouldn't get it as a first lens but for a second that is a good option if you notice you need to go wider.
XF 16-55mm f2.8 is rather heavy and for landscapes you won't need that f2.8.
Why not consider an X-T1? As long as you don't plan on shooting video or very fast AF situations (think sports) then that one will work as good as the other options you listed. Plus it will be cheaper second hand. The biggest difference would be the 16MP sensor instead of the 24MP of the X-T2 and T3. X-T4 and up has 26MP. Just know that 16MP is plenty, just compose your shots right from the first time and there is no need for more pixels.
Models like the X-E3 can be found new for 500 EUR. Downside of the X-E and X-T10, 20, 30 models is the different layout and the smaller viewfinder. Especially once you've looked through one of the models with the larger viewfinder you'll notice how small these really are. Difference in layout and buttons is mostly a preference, depends on what buttons (dials I should say) you really use a lot. Impossible to know up front.
I read you're not interested in those lower end bodies because of lack of WR. Stick to that for now but know that WR is really overrated. It's a gasket where the lens meets the body and then some more rubber gaskets in the construction of both lens and body. If you keep a jacket over your gear when it's really raining hard you'll be fine with any body/lens combo. WR is useful for traveling and very harsh, professional use of gear. For all the rest it's just a feature that sells.
New or used
There is really not much that can go wrong with these bodies second hand. Or at least not something you wouldn't notice when you try it out. If these break it's most of the time completely dead.
For the X-T1 there are some known issues like the rubber grip material separating from the body, the on/off switch and trigger switch sticking, the access doors bending for the ports... I had all that happen to my X-T1 and got it fixed by Fuji for a total cost of 350 EUR. These days you could buy a used one for that price.
The cheapest big viewfinder model they currently sell new is the X-H1 which you should be able to pick up for around 700 - 800 EUR (yes new). But they are getting harder and harder to find new.
And any other model used will be cheaper. I would go second hand. You can always buy a new model later one if you know you use it a lot (or if the second hand one finally breaks). At that point you'll know what to look for in a new model. And buy picking the previous year model during a sales action you can save a lot.
Just to get the most of it go for either the X-T1, X-H1 or X-T2 and forget about the X-T3 and X-T4. These bodies don't add much in terms of photography. Those are minor upgrades and more within the video department anyway. With the X-H1 and X-T2 having the benefit of way better AF (mostly for tracking) and 24MP instead of 16MP and the X-H1 having IBIS and the bigger grip and the always on screen.
Once you want to move up you can then use that body as a backup. Hope that helps and whatever you get, use it, a lot.