So long as it's the same preamp, which I believe it is, yes you should be getting the same tone coming out of the pre section. Now if you want it to sound exactly like what you're hearing in your headphones it may not sound identical. Your headphones may be coloring the sound to some degree unless they're studio monitor headphones made to not color the sound at all. Also, there may be some eqing going on at the board that you don't hear when just going through the headphone out and the room will have some effect on the sound coming out, since you've got quite a bit more space acoustically from speaker to ear that can cause a few different sound things to happen.
You might try checking out the thread over in the amp or effects section on using the B3 as a preamp because there are quite a few internal parameters that you may be overlooking that are causing you to get less than ideal results. I love they way my B3 sounds and I use it through the power amp of my PF500 as my pre. I think it's a top notch preamp, especially going straight to the board.
The B3 only falls short in that there's no way to initialize your patch quickly. You should make sure that in the total menu your patch is mixed 100% so you're not getting a bunch of raw bass, set the level on the page 100, go to the global menu and set the volume to about 60 and then on the amp sim set the level to 100 and scroll over to page 3 of your amp sim and see what the cab simulator mix is. Most amp sims on it are preset at 50%, which might sound good, but in my experience usually doesn't. If you want raw preamp sound coming through the system, set it to 0% mix, and if you want a mic'd cab sound, put it at %100, and then you can even scroll through the cab models to see if one suits you better than the original one assigned to it. By taking these steps when setting up your patch, you can be sure you're getting a healthy signal to the board. Also be sure that the pre/post switch isn't engaged so that you're not accidentally bypassing the amp sim all together.
I don't write this post to be insulting of course, merely because I realize not everyone is glued to the manual on something like I am and I don't believe that in order to get the best performance from your B3 you can just plug it in and twist a few knobs. Also, I think you may be trying to fix a problem by throwing more money into it, when it may be as simple as developing a better understanding of equipment you already have. If you've already written off the B3, that's fine. But, I think if you work with it a little, you might just find that you can get what it is that you're looking for.
