Because it's possible to add effects when drawing sprites like color switch and horizontal/vertical flip, I would like to be able to do it also with the map editor.
What do you think?

I believe color swaps should work fine on map() calls.

If you want more, it shouldn't take many lines of code to make function that mget()s a range of tiles and flips or fiddles with them before spr()ing to the screen. Most of what I can imagine wanting to do I'd want custom conditional code for, anyway.

(Basically the same way Jelpi handles pickups and such in its map- using flags to filter them out, and doing a pass to handle special things stored there.)

Sure, but It require a full scan of the map to check if any sprite has a flag or not.
An other option could be a custom function passed at the map() call to control how each tile should be render.
Anyway, If the built-in map() function is a simple lua function, there will be no speed gain at implementing such a request.