Experiment #1: Ocean Vs Flat Area Vs Mountain
I started with an untouched folder of DF_31.25_win. The advanced world gen parameters had not been changed in any way. The size world I was using was "Medium Region."
In Ocean embarks, I embarked on 3/4 land tile, 1/4 ocean tile. On Mountain embarks, I embarked with 1 mountain tile and 3 other ones. On Flat embarks, I found a 16x16 region that was as flat as possible and embarked near a river if possible. These flat areas were about halfway between the nearest ocean and nearest mountain, and as far away from them as possible.
I embarked in 2x2 spots and measured from the center of the wagon. These embarks were as far away from each other as possible, in their own oceans or mountain ranges.
This measures the number of z-levels total, measured at the very bottom of the circus.
Region One:
Ocean Embarks: -124, -64, -104, -108, -91
Average: -98.2
Flat Embarks: -37, -50, -52, -74, -58
Average: -54.2
Mountainous Embarks: -67, -82, -48, -54, -72
Average: -64.6
Region Two:
Ocean Embarks: -85, -105, -89, -98, -76
Average: -90.6
Flat Embarks: -37, -52, -31, -42, -38
Average: -40
Mountainous Embarks: -49, -48, -41, -44, -58
Average: -48
Total Ocean Average: -94.4
Total Flat Average: -47.1
Total Mountain Average: -56.3
Result: Oceans have the most z-levels, and flat areas are shallowest. I was very surprised at the shallowness of mountain embarks, though I had been measuring from a wagon which was at the base, instead of from a peak.
Experiment #2: Elevation 1:400 vs 99:400
For this experiment, I created another medium world. The changes I made were changing the minimum elevation from 1 to 99. I also removed the requirements of "Minimum Initial/Final Ocean Square/Region Count," "Minimum Partial Edge Oceans," and "Minimum Number of Low Elevation Squares," because these would cause rejections.
Again, this number is the depth of the very bottom of the circus counted from the wagon. I chose the locations in the same manner that I chose them for the first experiment, but there were no oceans this time.
Region Three:
Flat Embarks: -35, -40, -34, -37, -34
Average: -36
Mountainous Embarks: -42, -46, -38, -38, -38
Average: -40.4
Result: Flat areas are 11.1 z-levels shallower on average than the vanilla parameters; Mountainous areas are 15.9 levels shallower.
That is about the difference between region 1 and 2, due to randomness.
I'd probably need a much larger sample size to come to a real conclusion. I think I've gotten a bit of a pattern, at least.
I still haven't tested cave size, though I'm almost positive it does something un-related to depth.
TL:DR - Flat embarks tend to be the most shallow. Ocean embarks turned out to be deepest, against the common theory.
I still have no idea how people are getting embarks over 200 z-levels deep. None of my test embarks came close. I never got such deep embarks on my own games either, which are on smaller and pocket sized worlds.