1. How can I check for a certain tile at the beginning of the game and have the stream start automatically from there?
Option 1, obviously you could use a sprite instead of a tile.
Option 2, create a plan on the map that has a rule that loops through all of the tiles in the layer and adds a sprite where it finds your special tile.
Option 3, It may be possible to implement a single plan in your overlay map that looks at the other map that's active and searches through its tiles to replace the special tile with a sprite. Make sure you somehow only do this once per map otherwise you'll be doing a *lot* of extra processing every frame.
2. Is there a way to have a tile behave like some kind of container, like only entering from the top and not being able to exit from any direction but from the top again?
If you create a tile shape that's solid from above (and optionally, below) on the bottom row of pixels, solid from the right on the left row of pixels, and solid from the left on the right row of pixels, you might be close. But it will be odd because you will be able to enter the tile from the left through the left side. Generally, tile shapes have to be convex to make sense. But this might be good enough.
3. Is there a way to embed a text file into the .sgdk2 file?
Option 1: Add a new Source Code object (it can be empty or mostly empty), the use the "Embedded Data" menu, load whatever text/data you want to embed into the SGDK2 file.
Option 2: Edit the Project properties, and enter text into the "Credits" property.
4. Do have any suggestions that I should add to this? I've already got a "rotating-wheel-with-water-buckets" idea.
I haven't looked at the project yet, so maybe you already did something like this. How about a converter blocks that change the properties of the water hitting them -- for example, change it into anti-water that falls up. You can get pretty sophisticated pretty easily too. Like make one that changes anti-water into Oriental water that always falls east, but leaves regular water alone

. You could also make a sponge tile that turns into an absorbent sponge sprite as soon as any water hits it. It absorbs a certain amount of water until it can't hold any more, then falls to the ground and turns into a solid tile, maybe spewing out a little water from both sides when it does. And how about a tile that breaks a neighboring blue tile when it gets hit (by creating a special blue tile breaker sprite next to itself).