While there is no rule that refrain people to start playing at level 20.
4e had something for shadar-kai at level 1, to move thru solid objects. No problem.
Gamewise, there is little difference between phasing thru a wall and kicking a door.
Besides, there are trivial ways to block such "plot breaking" effects as divination, flying, phasing, and so on.
Make low-level spells like Protection from Planar (Evil and Good) able to routinely screen a room from divination, planar travel, ethereal phasing, etcetera. If cast every day for a year, the defensive effect becomes permanent.
Create an equipment akin holy water called "holy salt". Anyone, whether Wizard or Fighter or Rogue, can pour the salt in a circle to block planar penetration, or line the walls of a room.
And so on.
Make these tools available so the DM has a normal trivial way to protect the content of certain rooms, in order to surprise the players.
Make these tools available, so the players can have characters that can do cool stuff, like phasing thru walls and flying! Characters should do this stuff.
If for some reason the DM needs to safeguard something, there is a normal way to do it.