If the humans can TARDIS-proof a room, then why can't the obviously more intelligent species such as the Daleks, Cybermen and others TARDIS-proof their ships?
We have no idea! It's a new thing.
Like deadlock seals and "the sonic doesn't do wood," every now and then a writer or producer decides that the Doctor's technology needs to be limited. Sometimes it's done well, and sometimes it's done thoughtlessly.
In this case, the idea of TARDIS-proofing a room was necessary for a cool entrance effect, and it doesn't seem much thought was given to its implications. We haven't heard of this thing before, and that's why none of the Doctor's enemies have ever done it.
That said, the vast majority of the Doctor's adventures have not featured the TARDIS except as a way to show up. TARDIS-proofing your Evil Gravel Quarry of Doomsday Plotting would just mean the Doctor has to park a little further away and walk.
Clutching at straws, but it could also be that TARDIS proofing a ship could also affect the performance.
If, for example, you built something that stopped a TARDIS from getting in through time it could, on a Dalek ship, stop them from using time corridors.
The Daleks and Cybermen have spent countless years attempting tardis-proofing, using all manner of exotic physics and wibbly-wobbly, timey-wimey stuff.
UNIT just lowered their ceilings.
Maybe its because UNIT have studied the TARDIS in first hand, like when the 3º Doctor was stuck in the Earth. Maybe its because the room is in a temporal distorsion, like in the Angels Take Manhattan. UNIT find that temporal distorsion and said, "Let's make a Doctor-proof room for our nasty secrets!" or something like that. This may not be first time that UNIT try to take some restrains into the Doctor, like the Arton Sensors that figured in the 7 Season.