I guess one of my primary questions is this:

For maples that have a deep dormancy once the seeds are “dried” – they usually recommend warm strat, then cold, and sometimes, even a second warm and cold season, then coming up the following spring.

Is it the samara, or the actual seed coat on the seed itself inside the samara that is the culprit? If I ‘deshell’ the seeds and remove the samaras, does that help in any way with the process? I’ve done that with some dried A. palmatum seed and the samara does crack off like a nut shell.

Nobody?

Firstly let me say I don't know the answer to your question and would like nothing more than to be told I've got it all wrong by someone who knows and be educated.
Anyway here's my own thoughts for what it's worth.
I personally don't believe it's the covering of the seeds that prevent germination,that would seem bad engineering to me.I know we all soak the seeds to 'soften them' but I think really we're doing something else.I think the first trigger the seed needs is moisture,and we are making sure it gets that trigger....after all when a seed falls into a dry area it doesn't germinate,it would be foolish to.
When a seed falls from a tree it expects moisture to say ok it's safe not to go dormant.If it's also getting colder,I believe the seed either uses this cold snap as a timer,or more likely the embryo carries on developing(I'm not sure if the embryo is fully developed when it falls)
When you dry the seeds they will go into dormancy and await signals to say it's ok to wake up.I think expecting it to come out of dormancy straight into a cold snap and have it germinate all in one go is too quick.Maybe the seed needs confirmation of moisture first and will only finally develop the embryo during a cold spell.....hence the need for the warm strat.
As to why some seeds need 2years I don't know.Wether they need more reassurance or the embryos develop slowly or something else.
Hopefully this'll spurn an expert to chime in and say that's all rubbish and we'll all learn ha ha

So I did order a couple ounces of the 2010 A. triflorum seed and some fresher buergerianum. Of about 150 seeds, TWO of the triflorums have sprouted so far. I will give the rest more time as dormant maples can be wonky. Some may also sprout NEXT spring, so I won't throw them out.

The buergerianum are still in stratification, but I think I see the hint of a root on one or two (about 30 seeds).

Honestly I'll be happy getting one good specimen of each, but more would be nice.

As for A. grandidentatum, aka big tooth maple, aka canyon maple, fresh seed needs 60 to 90 days cold storage after it has absorbed moisture. All removing the seed coat would do is make it easier to absorb moisture, but at the same time you might make it rot I might nick it scratch it or scar it I wouldn't try and remove the coat the samara doesn't matter at all. It is part of the sugar maple complex but very different tree very slow in comparison and grows in hotter drier places. The first tree is my big tooth approximately 20 years old, probably 18 feet tall. next a Japanese maple I grew from seed 7 years old

Oh if you want seeds for Acer grandidentatum or leucoderme try and contact me late summer I'll get them for you.

I have also wondered if taking the shell off an Acer palmatum seed will speed up germination. That would be scarification I think.

there is scant information about why 90-120 days if cold stratification us needed for certain seeds. What does the coldness do, chemically, that triggers that little root to start pushing through.

Also, houzis point on the embryo. I also wonder if the embryo still grows in some way when it fall (or is removed) from the tree. And actually needs to be separated from the tree for a time before it becomes viable.

so far Acer palmatum seed I have picked straight from the tree in summer and put into cold stratification have not germinated.

My understanding is that there are germination inhibitors some kind if auxin or other plant hormone that starts to degrade once moist and cold for a period