I'm not sure what he put on and of course he is nowhere to be found. Any suggestions as to what to do at this point?

Cypress left on it's own will weather a nice natural gray. That's a red flag if you're dealing with mold and mildew. The wood may not actually be cypress. Or you may have a much worse problem than a cosmetic issue. Something is wrong here. A covered porch shouldn't be having any mold or mildew issues even if the wood wasn't a rot resistant variety. You've got some type of moisture infiltration problem that needs to be diagnosed before you worry about treating the wood that's there. Look to the flashing for the roof being done correctly as the first suspect. I have a 30 year old shed addition to our barn where the PO used plain old interior grade studs to support the metal shed roof. It's been mostly fine, except for the carpenter bees. Never molded or mildewed. I'm sure the PO did some type of ground treatment for termites though, as otherwise it wouldn't have lasted that long without the wood itself being treated.

Old-Growth heartwood Cypress is the decay resistant quality the type best suited for outdoor environments when left untreated.. This type is near impossible to find these days. Second growth cypress, the most common found at your builders supply lacks the same decay resistance and post-installation treatment is a necessity. You should treat the bare wood immediately. Use an oil-based stain / sealer which is most compatible with the natural oils in cypress. Acrylic based is also an option. I've been building Outdoor Showers in Florida for 23 years and can assure you new cypress does in fact mold, mildew, and decay when left untreated.

Could the reason for the mold be that the wood was not properly dried before it was sealed with stain/paint?

Digging up this old post in the hopes the OP sees it and can update with product used and what degree of success, or anyone else with updated info. As OP stated info online is conflicting at best.

We have 3 cypress porches around our house, decking with hidden fasteners and T&G ceilings, Douglas fir posts.. We have had no issue with mold/mildew on any of the ceilings. The decking and posts however have been a disaster, posts almost black, decking not quite as bad but bad. We are in western NC mountains at the edge of a temperate rain forest. Decks and posts were treated at install with Penofin Red Label Clear - seemed like a great idea at the time. Ceilings were treated with Australian timber Oil Clear but I don't know if it's the product that has kept them mold/mildew free or because they don't get wet like the decks and posts. We scrubbed decks and posts last weekend with a detergent/TSP/bleach mix, then power washed with clear water. Decks look great, posts are significantly better, might need another round.

Do we use the Australian Timber Oil and hope it works as well as it has on the ceilings? Research has turned up some people saying that oil products actually give the mold/mildew something to feed on and acrylic products are better. There's not a lot of info out there for cypress but it's still a rabbit hole. Leaving them untreated is not an option given our climate. They need some protection from water and significant southern sun. If anyone has specific product recommendations I'd appreciate it. We have some unused boards and can test if need be.

In similar situation. What did you end up doing?

@HU-763827390 Not sure the OP from 10 years ago is going to see your question and come back. I had a similar issue outlined in the post above yours. We opted to leave our decking raw once they were cleaned of most mildew with mixed results. Small back door porch floor gets mostly morning sun, has remained mildew free but looks a bit dry. Large sitting porch floor gets sun on the edges of the room morning till about mid afternoon, has remained mildew free and also looks dry. Front door porch gets sun midday on - strong afternoon, south/west sun - has remained mildew free but looks like cr@p, very dry, cracked and splitting in places. We believe the mildew culprit was the oil based product and have found information that mildew loves to feed on it. But we are also reluctant to apply a different, non-oil product and possibly go through the blackening again. We get lots of heavy wind blown rain and also strong southern sun. No clue what the best option is - sorry.

I ended up sing a bleach/water solution and then gently pressure washed off. After letting it dry a week or so, I used a product called TWP. (twpstain.com). I bought it locally from a cypress supplier and it was highly recommended. There are several colors but they all had a slight tint to them. (They don’t offer a clear). It turned out great and has started to fade a little in the column sides that see the direct sun after all that time but it has held up well.