When I first did the excel spreadsheet for building the regeneration time calculator I saw a lot of what you posted. But I will admit that my own testing before submitting it as a wiki page was limited to low levels.
The regeneration "bonus" you're supposed to use in the calculator is your aspect bonus that is shown in tool tip when you mouse over the aspect name on the combat arts panel.
This bonus, in my testing, showed expected changes from stamina distribution, concentration points spent, and appropriately spent focus skills as well as level ups.
I did not test high level characters nor high level CAs. I did spend CAs to level cap and find times don't diminish, only power.
The game does a lot of rounding when displaying the times and likely rounds and truncates decimal places in actual times but by how much, I don't know. The effects of rounding and truncation may become more pronounced as well as missing figures from my calculations as the numbers get larger with higher character and arte levels.
Edit: I just looked at the wiki page and it does say in the instructions to use the stamina tool tip. This will give incorrect calculations, as you pointed out.
Using the aspect regeneration bonus per the combat arte panel will give you the bonus to each specific CA after skills, stats, buffs, and gear, and is the value you're actually looking to use.
Here's some pictures that may help with the Wiki instructions.
Aspect regen bonus tooltip.
Runes read, slotted, and resulting regen time.
Maybe someone with some wiki editing skills can insert the pictures to help with directions. I've already updated the text.
Inputting this particular info into the calculator gives me a correct result of 0.538 seconds.