All of Chris Morgan's pipes have his brand on them except this line (i.e. Arbutus, Bones, BlackJack, One, Briar Cigar, and his Handmades). Different lines have a different stamp. These lines of pipes have stamps because they're all Chris' design. The reason he didn't stamp this pipe is because it's a collaboration with Sean Reum. As you noted, but stamp or not that will not affect the quality of the pipe and the smoke. Whether the pipe comes in a sock and/or in a box etc., none of that affects the quality of the pipe and the smoke. All pipes, whether high end or low end will require a break in period as I'm sure you are aware. As for the stem, that's all preference. Some pipe smokers prefer thin stems while others like thick stems. Some like p-lips and others like fish-tails. Just because a pipe came with a different stem than you're used to doesn't mean it's not a quality pipe, it just doesn't meet your specific standard. Which is fine.
I used to skype with Chris a lot several years back, and he's a super nice guy. If you contact him he might be able to help you out with a stem that will meet your specific requirements. If not, there are plenty of pipe repair shops that could make you a stem that meets your needs.
As for me, boxes and pipe socks are only good for shipping the pipe in. Once I have the pipe, I never use the box or sock again. Plus, if there is no fancy box or sock then it should help lower the cost of the pipe. I don't need to pay for fancy packaging when all I want is a nice pipe.