Programmer Tweaks is a tweak pack, so I usually make the least amount of changes I need to make to a texture to have it look how I want. It's kind of like, "how would a programmer update/tweak these textures?". The goal of Programmer Tweaks is not to make textures look like they weren't made by Jappa, even though many textures end up not looking like Jappa textures anymore.

I'll usually choose to either:

1. Tweak a programmer art texture to look more polished
   
2. Tweak a Jappa texture to undo excessive anti-aliasing or bring back what made the programmer art version so unique
3. I remake a programmer texture from the bottom up with an entirely custom palette and shading (this has happened for very few textures and netherrack was one of them)

In the case of cobblestone, I genuinely think the general shape and shading of Jappa's texture is nice, it just had really bad light levels/white balance. So I just tweaked Jappa's cobblestone a bit, and it now has the same amounts of blacks, grays, whites, etc. as the programmer art version but it has Jappa's shape and shading.

I did try to make my own polished version of the programmer art cobblestone... It's a lot harder than it looks though and my best attempt was still awful compared to my tweaked Jappa texture. It's just really hard to make the stones in cobblestone as flat as they are in programmer art without removing all shading. I might try again sometime though :]