If it were mine, I would build a new knee wall at the height of the windowsill. That immediately brings more calm to the room and hides the heating pipes at the same time. Then I would try to install the toilet pipe behind this drywall. The pipe would probably need to be routed around two corners. It’s best to ask the plumber if he can manage that with the necessary slope. I would extend the shower across the entire room width including the roof window. The sink should be placed next to the door with a continuous under-sink cabinet, which should then be approximately at the height of the windowsill.
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The effort would probably be quite high at first, because of the toilet. But if this is going to be my main bathroom, it would be worth it. However, if the plumber can’t manage the toilet, the plan is basically useless.