You are guaranteed to be able to reach every room and every item in every palace. It is guaranteed that there will be a path to the entrance or exit of the palace from every room in the palace, with one possible exception (see the Fallthrough section, above). Here are some tips for navigating palaces:
Keys that are collected in one palace can be used in a different palace.
If you fairy through a door then find a key, you can use Up+A to save that key instead of spending it to get back out.
If you try to fairy through a door when you have a key, you will still spend a key to get through the door.
Bosses and mini bosses drop keys that can be used in other parts of the palace.
If you need to, you can use fairy to get through the key door at the end of a palace and place the gem.
If a boss or item room is normally entered from a certain direction, it will still be that way in the randomizer. For example, in palace 1 you enter the candle room from the right, but you enter the boss room from the left. That means if you come to a room and have an option of going left or right, you will likely have a higher chance of finding the candle by going left, and a higher chance of finding the boss by going right.