I saw/read your post on my phone at work but, wanted to wait until I got to the hotel to respond where I have an actual keyboard..lol
The end offsets really depend on a few things..
Any end vise that may be in the long term plans. If you're thinking the BC set up, this requires a little more overhang. I don't recall the exact measurement off the top of my head but, it's a consideration. If you go with the Veritas or HNT, then the overhang doesn't matter. And, you'll want to do some more homework if you want to go with Andy Klein's turbo vise as an end vise which would be pretty cool!
Front or Leg Vise - If you go with a leg vise, you'll want a little overhang on this end to allow some design room for the chop.
So, figuring that stuff out should answer your questions about where to locate the top side to side.
Structurally, either is fine. I would look at the plans for the leg vise of choice and let that drive your decision. In the case of the BC hardware, you can download the plans without buying the hardware and it's a lot easier to cut the joinery without the leg attached. Even if you're not ready to spring for the hardware yet, this would severely pay off down the road.
Reality is that this M&T attachment is ultimately to prevent the top from sliding side to side. What I typically do is just take the mortise as deep as the router bit that I have on hand for the job and it's always been fine. I've never had an issue.
Assuming you're going with 8/4 material, what I did is only mill until they were flat trying to get as much material as possible out of each board. Doing this usually means you don't need the 1" thin board.
As for the gap, I would not do a 4" gap. I noticed recently that Marc changed his insert. He cut down the middle so that it was a recessed tray rather than a tool holder. He did leave the ends the standard height to act as a planing stop. I don't know if this is right for you as I think you use a great deal more hand tools than he does but, thought you might want to go take a look..
It's hard to tell from your drawing but, one of the most important things (IMO) about this bench is that the front of the bench and the base all be flush. This is what allows you to clamp items to the front of the bench. Either in a leg vise of clamps. As for the joinery on these connections, just about anything will work. I've done them with traditional M&T as well as Domino XV and not had any issues.
Couple thoughts in closing:
Top Thickness - I know earlier you mentioned the possibility of a 3" thick top. Again, just my opinion but, I would stick with hardwood and as close to 4" as you can if you plan to use hold fasts. I use them all the time and love them!
Dog Holes - Just something to think about in your design. Their location depends a bit on the tail vise that you choose but, it's much easier to take care of on an individual board rather than an entire slab! As for the round vs square debate, as far as I'm concerned, there's no wrong answer. I'll admit that I do like my square ones a little better than my round ones but, they both work just fine!
Storage - Not sure if you're considering storage? Of all the ones I've built, I like the storage solution in my kid's bench better than any other's I've done. Just remember to measure the hold fast depth before deciding the height of your storage solution.
The kid's bench - You may or may not know but, the plans for that bench are over on my website and free for the download.. https://www.kevswoodworks.com/plans-download
Sorry for being long winded, I just wanted to be thorough since you took the time to type out all the info ?