While my two wizards entered the waterworks together it is a known fact you can port to commons and not FLEE, but port to commons heal and return and enter and be where you left off. While one wizrd ported to commons and entered again ok, the other was placed in a different area of that realm stopping him from being in the same dungeon as his fellow wizard. I had to just abandon the dungeon because I dont want to take a risk of getting more into the dungeon and this happen again. With the different areas of a realm it messes up play. Can game tell me if they will ever get back to just realms with no areas? If you are looking at a different playing area when you port to somewhere like commons, it is ruining the dungeon process. Now port to a player and you will be in the realm that player is in. and area. For some reason the areas have things messed up in Dungeon play like waterworks. I have played waterworks for some time ported out to commons and entered again and took up where I left off, now that is not possible.
If your current server becomes crowded it will force some players to another server to compensate. Because some players were using an exploit, Waterworks does not allow you to keep your progress if you switch realms.
Now, as you stated, most dungeons will allow you reenter via sigil if you exit in a manner that doesn't reset the dungeon. Waterworks has the added exception. However, the intent has always been that you complete the dungeon without dying, fleeing, etc. Completing a dungeon solo or with minimal players is a sign of skill, but Wizard101 cheating dungeons have always strongly encouraged the use of four wizards and only their potions bottles to survive. Most MMOs have always required a group or raid to accomplish their most difficult dungeons.