I have theory about it (posted it long time ago).
Twilight Realm may LOOK like Sacred Realm, but not be it. It could've been made to look like SR, while not being exactly it.
If interlopers suceeded in breaking into SR (after which master sword was forged, to prevent others from doing same), shape of TR may be another part of their punishment - that they will be forever kept in realm so simillar to the one that they've broke into.