ProMods

Dunno how it's laid out in Blender
Don't you have a series of objects with different name? Either named Vis or Col
For signs a scaled dummy node might be used

I have a question about Blender. Is it totally useless now, since after 1.27 SCS have changed the entire game mechanics. I was hoping to use a free tool, instead of needing to buy Zmodeler3.

It's not useless. We use it all the time

I thought we would not be able to use Blender after they did some changes in the 1.27 patch.

SCS is using Blender Tools too, so they can't make it obsolete
Converting our map to 1.27 required converting the models/prefabs too and we used Blender Tools for it.

Wasn't that the whole point of Blender Tools? Officially supporting it so that you won't have to buy Zmodeler3 which needs to be updated first to work with the new format? Zmodeler3 isn't even officially supported, they reverse engineered the SCS formats. I remember 50K put out an update for Blender Tools and Conversion Tools a few days before 1.27 and people were all confused about the new format, turned out SCS was just a bit early with their update.

So... If I want to modify the ProMods map, I save my extensions, and how should I put the map saved to editor to continue the editing or playing?

You have to pack the sectors and put them above ProMods.

I have a short question: I read the part about the icon atlas and that every icon has it's definition but it doesn't come clear to me how to add icons to the atlas; I'm not sure if that's described; so my question: Is how to add icons (e.g. arrows) to the atlas correctly?

Check how currently existing atlases are created.
And it's all here: https://promods.net/viewtopic.php?p=118782#p118782