I am wondering if you are familiar with the way the SIEG X2 Y axis screw and nut are constructed? There is no way to "align" the nut. The manual tells you it is SUPPOSED TO move. They tell you to only "snug" its retention screw so that the nut is pretty much loosely held in whatever is the closest to a real alignment. Its poor design. They do that, coupled with the lack of a tail end carrier bearing, so the screw can move around "if needed".
It's like how some people only fasten one end, and the head screw, on a DRO scale, because they don't want to take the time and patience to properly get the scale fastened such that the head travels perfectly aligned from end to end with both ends and the scale head firmly screwed down. If you try to fasten the nut retainer screw tightly, the screw will bind at some point(s) in travel. My statement that the screw goes off parallel is an assumption, I admit, as it is forced in some direction by the movement of the acme nut in its loose holder, as it suddenly grabs in the slot. Ideally, wanting something to be able to move around in a slot should not incorporate the end of a screw trying to hold it in place, but should incorporate lubricated polished bearing surfaces to guide it along a desired path if it does move, precisely adjusted to eliminate chatter. Imagine if, instead of a nice smooth flat gib strip, the ways on the mill table axis were held in tight tolerance instead by only the tips of the gib screws themselves against the ways. That's essentially what SIEG did on this acme nut.
The X2 Y axis nut looks like an inverted tombstone. The threads for the screw are toward the rounded end. The squared off end sits upward in a slot that is wide enough to allow the tombstone to rotate many degrees left and right of being perpendicular. In fact, it can rotate beyond the point where it comes out of the slot in the carriage, if not careful when adjusting it. This allows for flexing of the screw (which ideally should never be needed) to accommodate whatever travel errors are occurring along the screw path, likely due to the fact the screw isn't rigidly constrained. This is a top heavy orientation. If the "snugged" retention screw loosens (it hides behind things you must remove to access it), the square top end of the tombstone "flops over" to one side or the other. Note that the alignment of the tombstone nut is the only thing holding the screw parallel to the ways, since the screw is free floating at the tail end. So when the nut tries to flop over, it pulls the screw sideways with it, and that is what causes it to bind, usually bringing a halt to any project until you disassemble, re-align and re-assemble things again. Typically, when the nut "moves" to one side, it never "moves" back the other way because of the retention screw grabbing at its surface as it slides past the screw end. That nut needs to be held in place vertically so it can't flop over. On the X axis, the squared off (heavy) end of its tombstone nut hangs down instead of pointing up, so gravity helps keep it centered. Perhaps what they should have used on the Y axis is a circular disc, with the acme threaded hole in its center, rather than the crazy inverted tombstone design they used. Hmm. I wonder if that idea would retrofit?
It is interesting you mention the X3 uses a tail carrier bearing. Perhaps they realized how essential that is. When they did, they should have applied the idea to any further X2 models produced. I've been through 3 different base castings along my upgrade path to the wider table and then a fixed vertical column. Every one of them lacks the tail bearing, and has this same problem with the Y axis screw binding. This "floppy nut" issue causing the binding is intrinsic to their design, it is not just a single incident on one casting. If they would have used the same design they use on the X axis, which has a bearing at both ends, and moves as smooth as butter, there would not have been this issue.