Hopefully you'll get a response about that specific design - which I have not examined; however, I think I can give you some general useful advice in answer to your questions;
An easy way to extract 1 villager from a holding cell is to run rail into the corner of the cell, and put a cart there. They glitch into the cart. For example, top down of a 3x3 cell of (probably glass) blocks B with a rail R;
B B B
B v B
B B R R R R ----->
If you use a powered rail, you can send a cart down and 1 will come back (if there's a few in there, anyway)
Green villagers are suppose to be useless; they're the village idiots, called "nitwits". They can breed just the same as others though.
Welcome to the world of villager breeding; they are an utter pain in the...neck... - they behave in awkward ways, "acting stupid", and doing exactly what you don't want them to do. It is perfectly normal to spend hours trying to get them into the right places, using water, blocks, rail, and so forth.
Don't worry too much about killing a bunch, it only stops them breeding for a few minutes.
Personally - having spent hundreds of hours on this - I usually manually move 'em around and just kill the ones I don't want, often using a sharpness axe (to avoid hitting others with sword), or with lava or flint+steel.
There are many clever and more elegant solutions, I've used those too, but they are really more for the look of things than the practical side; what I mean is, you can breed up the good ones without complicated systems, by just killing most until you get the ones you want - which, really, is a few farmers and a lot of whitecoats.
Anyway - I really think you should watch this, which is a really elegant way of sorting them out;
If you watch his other videos though, you'll see he goes through all the same pain, with glitch villagers escaping as he tries to push them around, move them with water, and so forth.
I know they can suffocate, which is why all the blocks they can glitch into are transparent blocks at head height. Blocks they can't suffocate in. Unless they're glitching through one wall and into the corner block, they shouldn't be able to suffocate at all.
They'll do that, yeah; or they will migrate through the transparent block and into the solid one, eventually. It's really annoying, but IDK any answer unless you force them to stay away, with water or something. Or put them in boats to stop them moving. (Not minecarts though, unless you block those in... they will make those move).
I have had a few disappear from the breeding farm, not quite figured out how that's been happening, but it's rare enough to not be a huge problem.
I'm not positive you actually NEED the glass blocks to let villagers see the doors, it may be enough to simply be within 16 blocks of them, but I'm a "better safe than sorry" type in minecraft.
They'll be suffocating, Sometimes when you reload the chunk, they glitch sideways a bit; they can migrate into the neighbouring blocks.
Regarding the second part, they don't need a line of sight to the doors, at all; they just need to be within 16 blocks; they can be totally enclosed in solid blocks.
I'm absolutely sure. Most iron-farm designs have then encased...although I guess they often show it with glass on the top, to make it easier to see where the vills are. But I've got various designs with the villagers totally out of sight, working fine.
I just checked out the mod, the description seems to indicate that it "visualizes" village marker data sent from the server. Wouldn't that mean that if the server doesn't supply it, I'm out of luck?
Or did I just misunderstand? It seems a little strange that something purely based on object positions would need to depend on server data.
The status of villages isn't purely based upon the current positioning of things; it can be affected by the order in which the objects were placed, and when houses were detected.
For example, you could have two villages spaced well apart, say 100 blocks, then add another valid house somewhere near the middle - it will join to the closest village. You could then destroy the rest of that village, and then put another valid house even closer to the other village, without them overlapping.
That, in a nutshell, is how these very fast "overlapping village" iron farms work, like the Titan, etc.