What keeps certified GA aircraft from being affordable?
Low volume, high liability, and the overhead of certification all contribute to the high price of factory-new aircraft.

Certification

The process to design, build, and test an aircraft to receive a type certificate from the FAA adds time and cost to any new clean-sheet design (substantially more cost if the design is novel in some way).
The design and construction techniques must conform to the requirements in the FARs, and you have to demonstrate conformance to FAA inspectors (who will also want to see you assemble a few planes under their oversight before issuing you a production certificate to go ahead and make them on your own).

Volume

50+ year old designs like the Piper PA-28 and Cessna 172 that are still in production on an approved type certificate avoid that cost, but are still a low-volume high-touch product: Here's a wing being assembled.
Because of the relatively low demand (and thus low sales volume) the cost of the skilled personnel to build aircraft isn't spread out the way it is with cars (and the investment in large-scale low-touch automation isn't economically feasible). That drives up the manufacturing cost, and the price goes up with it to ensure the manufacturer is still making a profit.

Similar economies of scale affect all the third-party parts going into new planes as well: radios, instruments, lights, etc. that conform to applicable FAA Technical Standard Orders (TSOs) are rather expensive.

Liability

Finally, any new aircraft starts a new 18-year liability period for the manufacturer. Any accident that results in whole or in part from manufacturer errors, omissions, or negligence in a new aircraft can come back to haunt that manufacturer in the form of a lawsuit, so the cost of product liability insurance is baked into the price of every new aircraft. (After 18 years the manufacturer is off the hook thanks to the General Aviation Revitalization Act.)

All of these factors take the Searey from being a \$50,000 kit (airframe, engine, and propeller) to a \$150,000 factory-built Light Sport aircraft, and that is putting it on the market as a Light Sport aircraft under "consensus industry standards". Producing it as a Part 23 certificated aircraft would add the additional cost and requirements of FAA certification.
(I'm using the Searey as a convenient example since you mentioned it in your question and I could find kit and factory-built pricing easily, but other light sport aircraft available in both kit and factory models seem to stack up similarly. I don't know of any that have been subsequently "upgraded" to a Part 23 aircraft: Only a few manufacturers have successfully launched that sort of product, and those command rather substantial prices on the new market.)