Unfortunately the manufacturing cost for the plastic enclosure is really what determines the price. I've been toying with the idea of designing an FPGA based drop-in replacement for the Atari 2600 circuit board. Something like that could probably be sold for about $150 or so, and it retains the Atari 2600 styling since you are using the original 2600 enclosure.
I started this project not to sell a product and make money, but rather to create something that I wanted. I think that the Walkman motif works very well. It's compact, and it's something I can set on my coffee table, and play Atari 2600 games on my big screen TV from the comfort of my couch. Plus I think that the "PLAY" button is a cute pun. The connector placement is not an issue since the game console is right in front of me. The only long cable I need is the HDMI cable that connects to the TV.
To answer your other questions, I used some styling cues from my Sony Walkman Pro, and that's where the tiny switches came from. The PLAY and STOP buttons simply turn the power on and off. I had thought about adding an eject function to the STOP button, but that made the mechanical design a bit too complex. And finally, I still want to add some kind of logo, and some lettering around the buttons that indicate their functions. I'm leaning towards dry transfer, but I'm not sure how well that will work on 3D printed material. It's on my to do list.
The 2600 core timing is always running at the exact rate of the original Atari hardware. I'm using a triple buffer to frame sync the 2600 video timing to the output video timing, and the horinzontal scaling is always an integer multiple of the 2600 horizontal resolution. The vertical scaling, on the other hand, uses what's called a polyphase interpolating filter to scale from 208 or 224 lines, user selectable, up to the output resolution which can be 480, 600, 720, 768, 1080, or 1200 lines.
One day I might experiment with trying to V lock the output timing to the 2600 timing, but for right now the delay through the triple buffer doesn't bother me.
208p * 5 would output 1040p with a thin black area on the top and bottom for 1080p displays. 160h * 9 would provide 1440 horizontal resolution with very close to a 4x3 frame size and ideal 1.8 pixel aspect. This would be an ideal display setting (with black borders) for NTSC games @ 1920x1080p60. Scanlines at 5x would also look great if you used 50%-100%-100%-50%-0% for the relative intensity.
As much as I love the look of the "Walkman" enclosure, if the enclosure is adding considerable cost to the project, ie contributing more than 30-40% of the BOM (bill of materials), then maybe consider redesigning the PCB and cart socket to use an off-the-shelf project enclosure. Some companies may even be able laser cut a rectangle slot for the Atari carts so you don't have to "Dremel" it out yourself.
I know that a "black box" styling isn't your vision for the Atari FPGA, but if it represents a significant reduction in price, I would be all for it. Currently at upper $300+ range, it's out of my budget, however I would quickly change my tune if you could offer something like a bare board kit for around $200 or less that let's DIY people fabricate their own enclosure. I could even see myself cramming the FPGA Atari in a cigar box or something.