By defeating Kain in the Chronoplast (see The Aftermath of The Chronoplast), Raziel would have gained the ability to shift into the Material Plane regardless of whether or not a portal was available.
Like many of the other deleted elements of Soul Reaver, Shift-at-Will was described in issue 19 of PSM:
About two thirds of the way through the game, Raziel will discover (in a secret area) the ability to shift between spectral and material at will; he no longer needs to find a planar portal to shift into the material plane. He still needs to be at full health, however. With the ability to shift at will, the game opens way up for the player. Raziel can now access the Sound Forge, the Sound Glyph Altar, and the Force Glyph Altar, as well as now being able to get inside the mysterious Undercity lair of the vampire worshippers. Other secrets and bonus areas are now also open.
The implication is that the portals immediately on the other side of the entrances to the Sound and Force Glyph areas were added after this ability was removed from the game, in order that they would still be accessible by the player.