Well, in the case of lockpicking and trap detection, I think it is somewhat easier to pick locks and detect traps with the proficiencies than it was before them, although that's tough to put a finger on because I completely rewrote the dice rolling mechanics with them so they work differently now.
With everything else it kinda depends on how you look at it. Many things that were slated to be moved to mods before were kept because I designed the proficiency system to protect them. Knapping and things like that are hard to do unless you know how; rather than make a neolithic tools mod and stripping them from base game, we added a system for knowing how.
After that, we adjusted recipes as we have wanted for years, to represent roughly the fastest you can make things. Then we added nonproficient modifiers to represent the fastest you're likely to make things if you have no idea what you're doing. You could see the proficiency as a penalty, but really if there were no proficiency, then the base time to craft these things would be way longer.
If we didn't have silly stuff like sewing a backpack from rags in ten minutes to start with, in a game about post apocalyptic scavenging, this wouldn't be much of an issue.
A better way to see the benefit though is to consider what we're trying to fix. With proficiency we can fine tune crafting time based on what you know, and we can allow all kinds of complex things that were unreasonably difficult to be craftable with the right stuff. However we are also solving the issue of being able to max out skills in two weeks, in a few ways. There are more things to learn, most of which are much faster to gain than a skill level would be, and learning them provides (often) a bigger and more tangible benefit as well, but to a smaller range of recipes.
Before stable I am hoping to implement at least a small portion of my "books helping proficiencies" proposal where you can get partial boosts to proficiencies from books, mitigating most of the remaining nuisance portion. It might be beyond my coding powers, we'll see. I'm also hoping to use the same code to make it so that as you progress in a proficiency your penalties are reduced, so 90% proficient would reduce your time and fail rates, but that has a lot of bug potential so it's probably going to wait until after stable.
Tl;dr: Mostly proficiencies don't buff things, but that's because previously crafting and skill gain were severely broken. However I am aware that we should have ways of learning proficiencies besides bumbling around trying to figure it out, and we (maybe even I) plan to fix that and improve some other bits.