Changing the game to allow you to would also be vastly more complicated than simply fixing the digging and construciton borders.
I think they are fixed, but not for multi-tile embarks. They were fixed so that sieges could not be blocked from entering the map, and to not have them from entering through holes you dug to the edge of the map.
Also, with the holes in the walls: why not obsidian cast them away with raised bridges picking up the slack where you can't build walls?
re "Fixing" sieges:
1) Why
shouldn't you be able to stop sieges from entering with a giant wall?
2) You already can anyway with bridges, or even with a wall 5 tiles back from the edge. So it's not actually accomplishing anything. Just let people do what they want.
3) There's already an option in the .ini for turning off sieges anyway. So obviously he doesn't care about people who don't want sieges being able to not have sieges in the first place.
re obsidian/bridges to fill holes:
Why not?
1) Most architecture in game isn't made out of obsidian or bridges. If you want to maintain a consistent style and architectural design (like, "i'm making a clay castle" or whatever), then it's impossible, but it shouldn't be impossible.
2) Casting is about 100x more effort than building, yet there's no practical justification I know of for it needing to be any more effort at all. Bridges less so but still far more effort than walls when you take into account the need for mechanism links to make them raised. This might all be fine if there were a reasonable need for the extra effort, but it isn't fine if it's just an arbitrary minor coding bug/mistake.
3) It isn't remotely realistic (in a real world OR a fantasy world sense), and in a simulator game like DF, lack of realism is in and of itself a problem, even if there were no gameplay issues. Because it breaks immersion and RP and makes it less of a simulation.