Is there no way of building a BSP out of it? I don't see why it has to be Euclidean to be partitioned, and loops are also possible (e.g. Deimos Lab). (The coordinates are definitely a blocker, so this question is academic.)
The “sectors” in the resulting level data have to be convex for the doom engine. The “asset pipeline” handles that by breaking up non-convex geometry into smaller convex sectors. So, there are no loops or holes in the actual level data, also from the cursory glance both of the large loops in Deimos Lab are actually not complete loops, but they have a place where the loop is broken. But that does not matter that much, as almost any level contains geometry that is either concave or has a hole (courtyard in E1M1, both large rooms in MAP01…)
The Doom design starts with X,Y,Z and then finds your BSP node. You can't warp to a different X,Y,Z without some type of warp portal which doesn't exist in Doom. Modern Doom forks have this feature and also have graphics portals so you can implement this (as MyHouse.pk3 does).