It turns out that 2.1.15 Software changed the way Lower Unpegged works. In Doom and previous versions of SRB2, the lower texture is aligned with the ceiling above the lower floor. In 2.1.15, it's aligned with the lower floor itself. The problem is that until recently (March 19th),
the description of Lower Unpegged on the Doom Wiki was incorrect. As you can see, this describes the behavior as you see it in 2.1.15, instead of what actually happens in Doom. The description of Lower Unpegged on the SRB2 Wiki is based on this description and therefore also incorrect. This is why I thought the behavior in 2.1.15 is "correct", because it matches with the description on the Wiki. The commit that changed the behavior in SRB2 was made by RedEnchilada, so I'll have to check back with him and clear up whether this was an intentional change or whether he made the same assumption as me that the description on the Doom Wiki is correct, and was just trying to "fix" an error that wasn't one.
Either way, you can easily correct the misalignment of your example in 2.1.15 by removing the Lower Unpegged flag and instead adding the Peg Midtexture flag.
EDIT: Oops,
didn't see Red's post in the bug report thread. Anyway, I already changed the pegging behavior in ZB's Visual Mode, so from the next release onwards it will look like it does in 2.1.15. If the devs decide to change it back or make any other change, I'll adjust ZB to match.