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Which actual products? Velfac/Rationel/Internorm/IdealCombi etc?
If you absolutely cannot avoid having to join and seal two disparate frames, then I would use two strips of expanding foam tape such as Ilbruck TP600, in an appropriate thickness. This will act as a weather seal and airtightness layer.
But having said that, why don't you just get the doors, transom and window made as a single complete unit?
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Klar windows - estonian company https://klarhome.com/
They don't offer that service (which is part of the reason they are so cheap). I will see what my builder says. He's not a bodge type really. I'll see if I can figure out why he's opposed to a transom.
they are timber windows with alu cladding.
I'll be using airtightness tape on all the window fittings, but i can't see how that could be applied to two window frames. Maybe on the exterior rather than the interior?