It appears that 251 minutes was a typo on TheDigitalBits' part - the actual runtime is 215 minutes, or 3 hours, 35 minutes. Compared with the DC's 3 hours, 6 minutes, that's 29 minutes added - Tales of the Black Freighter is 38 minutes long, so that's 9 minutes cut from TOTBF, at the very least. Bear in mind that additional footage has been added to transition to and from Black Freighter.
So I guess it's not so much a cut-and-paste job, and they're actually cutting it to make it work within the story.
And seeing as how the final run time is about 3 and a half hours, which is what I was aiming for at the maximum, I will not be doing two versions - it will be just one, with Black Freighter intact.
I think this runtime news also means that none of Into the Hood has been cut into the "Ultimate Cut," as some had speculated.
Don't assume that all you'll have to do for your version is cut down extra stuff. Start by adding the extra pieces of Black Freighter back in where possible and filter Into The Hood in wherever you can too, then start your cut.