Most of the original levels are normal and everything about them is defined and configurable within the xml.
However there are a few exceptions, where the game exe is coded to do things a little differently. These tests and actions cannot be changed in the exe, so you will need to account for / avoid them as necessary.

The following are all the known “special” things.

Genetic Sorting Machine Music Change

If the level id is GeneticSortingMachine, then when a Beauty ball pops the level music is changed to a resource called SOUND_LEVEL_GENETICSORTINGMACHINE_ALTERNATE

Beauty and the Electric Tentacle Signpost

When a signpost with text="SIGNPOST_BEAUTYANDTHETENTACLE_3" is read, this unlocks a Steam achievement.
Note: This appears to work even if the signpost is in another level.

MOM

There are (obviously) many special things in this level, so many in fact that it really deserves its own page. [TBA]

Deliverance : Access denied Popup

When the player attempts to play a level with id Deliverance the game checks whether the "Terms and Conditions Accepted" flag is set in their profile.
If it is the level plays.
If not then a Popup Message box appears instead, which only allows the player to click OK, and the level does not play.
The popup uses the following Global Text resources
DELIVERANCE_BLOCKED_TITLE , DELIVERANCE_BLOCKED_BODY , DELIVERANCE_BLOCKED_BUTTON_TEXT

Undelete Pill

When an UndeletePill goo ball pops, the game displays a popup message (described in detail below) When the player clicks either button, the game executes the command undeletenow, which does the following.. in this order...

Modifies a linearforcefield
It enables a force field called skeletonfield (see Deliverance level).
Obviously if this field was already enabled then this has no effect, but if the level does not contain a linearforcefield item called skeletonfield, then the game crashes.

Switch to "movie" mode
It displays the letterbox bars, and prevents any further interaction with the Goo Balls, and prevents clicking on the Continue Handle, if already down.

Moves the camera
It pans the camera to a fixed position 0,1000
Pauses for about 5 seconds then pans again to 0,5550.
The camera will not leave the scene so if scenebounds maxy is less than 5850, then camera will stop when it reaches the top of the scene.

Sends an internal message : END_DELIVERANCE
If the level end condition is set to endonmessage END_DELIVERANCE the level ends normally.
If the level end condition is set to anything else… then the level is now stuck, and the player cannot finish it..
or retry or quit.

Undelete Pill Popup
Uses the following images and sounds.
IMAGE_GLOBAL_UNDELETE_DIALOG res/images/popup
IMAGE_GLOBAL_WIDEBUTTON_OVER res/images/widebutton_over
IMAGE_GLOBAL_WIDEBUTTON_UP res/images/widebutton_up
SOUND_GLOBAL_DIALOG res/sounds/popup

And these global text resources
UNDELETE_CONFIRM , UNDELETE_CONFIRM_TITLE , YES_BUTTON_TEXT , OK_BUTTON_TEXT