The best idea I can think of uses text box space and however many tile types as the screen with the most warps in it uses.
So if you need 5 warps on a screen you have to use 5 tile types to do the warp so it can grab what ID the tile is.
Then instead of text in a text box (and corresponding text group) you have an array of bytes pointing to each screen.
This leads to a space problem all its own though: If you have 16 screens that warp you're going to need to use 16 text boxes to hold the warp data, and 16 text groups for those screens to reference that data.
Because NESMaker is designed to make many kinds of games, the more specific the feature you want the more work you're going to have to do and sacrifices will have to be made.
It can definitely be done, it's just going to take a decent amount of work and something will need to be sacrificed to make up for the space we need to store that data.