Abroad registered Yachts in US water

In general, a foreign-flagged vessel must vacate U.S. waters for a 15 day period annually to be issued another 1 year cruising permit. An exception exists for a vessel that has had duty paid, or is U.S. built, and is owned by a U.S. citizen, living in the U.S. , although sometimes with difficulty. When renewing the cruising permit for a yacht that qualified, I sometimes found that the local U'S Customs offices weren't necessarily familiar with the exception. I carried copies of a letter from the Customs Director that was an internal guideline explaining the exception that I would provide at the local offices. The local offices would then call Washington and have the contents of the letter confirmed, prior to issuing a renewal of the cruising permit. Both Miami and Fort Lauderdale are familiar with the rule.

Never had a problem with Customs officials in Baltimore, Virginia Beach or Savannah. Obviously there are other offices that know about this - considering they deal with more commercial vessels.

Funny about that; Baltimore is actually one of the places I had the most difficulty with. There and New Haven. It probably just depends on who you get.
The guy in Baltimore was REALLY reluctant to issue the cruising permit, even after he called Washington, D.C. Made it sound like he was doing me a big favor and against his better judgement. He even went on about how the permit could still be revoked. I just smiled and "Yessir"-ed my way through the process. I wasn't the yacht owner, so it was just another day, another dollar, for me. If it didn't happen, I would have rented a car and gone to another office.

Because of my maths biased thinking, I don't fully get your combination of "and" plus "comma" plus "or":
a.) May we keep a foreign-flagged AND foreign-owned AND US-built vessel in US waters more than 12 months because the vessel was built in the US?
or
b.) May we keep a foreign-flagged AND Delaware LLC-owned AND US built vessel in US waters more than 12 months because the vessel was built in the US? (LLC owned by foreign-persons)
or
neither a.) nor b.)

Google "Maritime Law Firm".

d.) an exception exists for the given circumstances I am familiar with. There may be other situations that qualify, including those you're inquiring about.
In my experience, it is best to have an official statement from U.S. Customs and Border Protection at hand when renewing a cruising permit, in the event that the officer at the local office is not familiar with all aspects of qualifying circumstances.
Marlin Magazine notes in an article that the rules for cruising permits "are open for interpretation". I have found this to be true.
U.S. Customs and Border protection can be contacted via this LINK

You can keep a foreign owned yacht that is Delaware LLC owned and Delaware registered (flagged) in the US indefinitely and Delaware registration is super cheap.

I have a foreign vessel at my private dock. It's been in the US for years, but owned by a US citizen (if that has any meaning anymore). It was formerly at a nearby marina. After a year the marina manager couldn't get the laws and exceptions thru his head even when presented with a copy of the laws, so we moved the vessel over here. Expect some trouble. Bureaucrats and apparently some marine managers have never held a real job.