I'm using that texture from the Wad of Daikatana ep1, taken from Quaddicted's wad bank. After checking the vine texture it had the wrong background color (it seems like this is a common problem in Quaddicted's wad bank), so I fixed it and run it. Darkplaces still doesn't recognizes the transparency (is there a commandline that can fix this?), but Quakespasm runs it like it should:
http://image.noelshack.com/fichiers/2016/02/1452527281-spasm0000.png
http://image.noelshack.com/fichiers/2016/02/1452527283-spasm0001.png

Also lighttorches I underestimate them once again. 2stronk4me.
Speaking of light, fog comes out fine in Quakespasm but is non present in DP. Same thing with the sky texture, it's all black even though I put lights (sunlights still have light and shadow issues with ericw's compiler it seems, or the small sky openings in the cieling make things fuzzy somehow). What the hell 

Does not support alpha textures. That is the reason you need an external tga file 

 

"14 new posts! This gonna be goo ... oh." 

So I don't know what the hell is going on. My start map is as for now divided by 2 sections: a short cave section, and the skill portal room. No matter what I do (and by that I mean changing light torches' light values, deleting some, up to just deleting all of them), the cave will always be flat-litted, but as soon as the skill chamber show its nose WHOOPS strong shadows and sunlight-quality shadows (At first I did add in sunlight2 but I decided to take it out because there wasn't any impact lighting-wise).
Just look (also in those shots light torches in the first section are supposed to be deleted, and worldspawn's light value is set to 170):
http://image.noelshack.com/fichiers/2016/02/1452545720-razenkrauft20160111214603-00.jpg
http://image.noelshack.com/fichiers/2016/02/1452545717-razenkrauft20160111214611-00.jpg
http://image.noelshack.com/fichiers/2016/02/1452545720-razenkrauft20160111214655-00.jpg
http://image.noelshack.com/fichiers/2016/02/1452545718-razenkrauft20160111214744-00.jpg
http://image.noelshack.com/fichiers/2016/02/1452545721-razenkrauft20160111214753-00.jpg
Also, somehow removing the fog key from worldspawn made the skybrushes visible again in DP.
I don't get it. 

are you using for your lights?
It looks like delay 3 lights(no falloff at all) from afar to me.

Use delay 2/5 for best results, also add the -addmin switch to your commandline for tyrlight. 

I tried to delete all lights (and I mean ALL light entities) this time to see what happens and
http://image.noelshack.com/fichiers/2016/02/1452548500-razenkrauft20160111223743-00.jpg
http://image.noelshack.com/fichiers/2016/02/1452548502-razenkrauft20160111223751-00.jpg
http://image.noelshack.com/fichiers/2016/02/1452548502-razenkrauft20160111223800-00.jpg
http://image.noelshack.com/fichiers/2016/02/1452548500-razenkrauft20160111223817-00.jpg

This still happens if I put -addmin in the light command
WHAT THE FUCK 

outdated lit files with the same file name get loaded by the engine anyhow, resulting in things like this.

http://www.quaketastic.com/files/hollow_odds.jpg

Check values on worldspawn in your map that seem conspicous to you. Even a "sunlight_color x x x", or a "light" value.

Delete those too, report back. 

Some engines in some machines don't like 0-255 values for fog, you have to use 0-1 (like 0.2, 0.5, etc) for best compatibility 

 

fog was already set on 0.3. It showed OK on Quakespasm but somehow not in DP.
A light key of 170 was still active in worldspawn, so I deleted it, just like the lit file (which I deleted once when my lighting problem occured, but it changed nothing).
Now though, after compiling (with the -addmin key still in) now everything is flat-litted (which is brigther than the initial value of 1170, so I assume it went back to 300), even the skill chamber.
What now? 

Dont use the worldspawn "light" key. Ever. It is better to start with a totally dark map.

It seems you have problems in doing what i adviced you to.

Are there any surface lights you may have overlooked?

To make this more clear. A map with no lights and a worldspawn "light" set to 0 should be rendered fullbright when loaded in engine.

So, assuming you deleted all lights and that worldspawn key, plus lit file, you should now see a fullbright map in the engine.

Now,as a test, put one torch in, and recompile. Report back.