It isn't really a bug, it's a competing game-mechanic. Better Beginnings specifically alters the early game by changing how you progress prior to the capability of smelting metals. At that point, it doesn't really interfere anymore (aside from altered chest recipes, covered more below).
If I were willing to accept that it invalidates the use of the flint tools in Tinker's Construct, there really wouldn't be an issue. But for me, I like being able to start with the TConstruct flint tools.
With Better Beginnings, you would progress by getting some flint from gravel, some sticks from saplings, and some leather strips from cow-boxing.
Then you'd upgrade to bone after mugging a few skeletons. At that point, you could harvest stone, copper and aluminum I think.
At this point you should then be able to advance normally up Iguana Tinker Tweaks metal progression.
Keep in mind though that BB also adjusts the recipe for simple chests too, requiring not only wood but some leather strips and IRON NUGGETS to craft. This means your ability to store things outside of any backpack type mod you may have is really limited.
All in all, you really have to want to embrace all those changes to enjoy it. I don't mind a harder start, but for me it is just a little too many things piled on top of each other.