(See the best response by Ndangerman.)
How do I make the 'start.dmi' be transparent?

icon = 'floor.dmi'
icon = 'start.dmi'
icon = 'wall.dmi'
density = 1

icon = 'player.dmi'
loc = locate(/turf/start)

Problem description: Empty 'start.dmi' ends up being a black tile in the map.

In old versions of BYOND I would just make an 'empty' icon for it and put it on the map, and it would work perfectly. Now, it deletes/changes the tile, in this case the floor.dmi, to a completely black one and puts the player correctly where it should be.

I'm using the DM Guide.
Best response

Keep ctrl pressed and then place the turf on your map.

Thank you, Ndangerman, it worked.

Now, Is there a way to make it visible on the map editor?
Imagine a game where there are a few start turfs(1,2,3) for respawn purposes. Or a game with teleportation from one spot to the other, changing maps, etc...

It can get complicated If I cannot see the invisible turf on the map editor.

If you want to place objects on the map in the editor that will never show up at runtime, you can set the object's invisibility to 101, or pretty much any high number, so long as the player's see_invisible variable is below it.
Alright, thanks.
In response to Kaiochao
In this case, it may just be a better idea to set the icon to null in New(). Otherwise, the underlay of the turf beneath the start turf will also be hidden.