I've found y-junctions to be a bit of nightmare myself especially when using complex profile walls with linings on them. The linings often cut through or the walls done trim properly no matter how I fiddle with the reference lines. I often have to resort to applying a 2D fill over the walls to hide any unconformity which makes it look okay in plan view - as long as they are looking right in 3D.
V12-V27, PC: Ryzen 9 3950X, 64g RAM, RTX5000, Win 11