Reading through old posts and came across information that 2005 and later models, Fountain used composite stringers (quoted by RG3). Assuming transom is still wood, however.

The 32's do sit really low at the rear. I've seen the rub rail in the water with 3 or 4 people hanging out at the rear. Even seen water up to the bilge blower outlets.
However my 27/29 (w/twin BBC's) has the rub rail abt 6-8" out of the water. The only time the rub rail is in the water is when launching from a steep ramp. The joint under the rub rail is supposed to be sealed however the sealant can shrink and pull loose from one side over time. When water does get past the rub rail joint, it drains into the bilge thru finished holes in transom on both sides near gunwales. The exhaust pipe holes on a 27/29 are well above the water line but do receive a lot of splash. They can be a source of water intrusion and should be properly sealed.

I fixed the blower issue by glassing them closed and running the vents out the side.

Look up the hull separation issue that formulas have had, that isn't cool either. Moral of the story is a old boat is most likely going to need something fixed. To tell you the truth if you find a fountain with a bad transom use it to knock the price down. If you can at least do the de rig and re rig it isn't bad and when done you will know what you have and can make some improvements in the rigging.

And yet his old 32 three hull numbers off was solid as a rock even with being exposed to a LOT of water, go figure.

Remember though, the top of the hull at the transom is not perfectly sealed at the factory prior to deck installation. (I've been to the Fountain factory many times.) And this is not unique to Fountain powerboats. When water gets into the joint at the swim platform, it can get down into the transom. That said, the main route of water intrusion is the holes cut for the exhaust tips.

The problem with boat manufacturing (and boat manufacturers) is that due to the low production volumes and lack of hard tooling in many cases, quality and process control is nowhere near what we've come to expect from other forms of manufacturing - like cars and trucks for instance. This leads to lots of process variability and thus a "good" boat coming off the line just before or after a "bad" boat. If cars were still manufactured this way, we'd all be crying the blues. (Full disclosure: This comes from a guy with 35+ years of manufacturing experience.)

do all manufacturers suffer from this issue…fairly certain cigarette fiberglasses the top and bottom halves together. would think this technique would eliminate the issue?

!!!!!

PM Glassdave, he has put stringers and transoms in both. He will have your best answers to your question.

With the molded platform it’s not possible to get in to the joint and glass the cap to the hull on the fountain.
it seems like older fountains (93 and older) are typically ok unless neglected.
Everyone I’ve looked at or worked on built mid 90’s up to a 2009 had rot.
looked at a few center consoles recently. Same thing. Couldn’t find a dry piece of wood in the boat.