From the wiki page on the Tacoma:
"The Tacoma was introduced in the US in February 1995 (with a market launch in March 1995) as a replacement for the
Toyota Pickup (which was the name used for the Hilux in the North American market). When comparing with the Hilux, the Tacoma receives engineering with
greater priority on ride quality, handling, comfort, and safety over ruggedness and payload capacity. The design intends to better suit the needs of the US and Canadian market, where pickup trucks are used as personal vehicles rather than for commercial, agricultural, and off-road purposes."
It appears that this coincided with design and engineering being done in the US also. It would be interesting to know where those engineers came from, and if they had experience building trucks! Anyway, flexy frames on pickups were the norm back then, and still are on >1 ton domestic pickups and any cab-chassis, so it isn't a weird choice. The payload bit has nothing to do with a flexible chassis, but has everything to do with a soft ride while unloaded. Also, regarding "safety" our US standards require that a frame be able to crumple in an impact, absorbing energy to reduce the G-force on occupants. The older Toyota trucks were notoriously poor at this. Obviously the decisions made to cause crumpling during impact are somewhat at odds with making a frame stiff and light. I expect that the wimpy last few feet of the frames is designed to be the crumple zone for rear impacts... or at least it's a side benefit.
The Tundra in particular is a low volume model, and simple economics will tell you that Toyota can't afford to spend too much on engineering. Back in the early 2000s I think they believed sales would be higher, but it became obvious that insurmountable buyer attitudes would prevent that, so they did what needed to be done to make it profitable... meaning the truck wasn't really updated for 15 years.
At any rate, the frame might be flexy for whatever reason, but it isn't weak. People abuse and overload the Tundras like crazy and they have a good rep for tolerating it. The flex doesn't hurt offroad ability either as I helps keep tires on the ground. Honestly, I think it's totally fine off road, as I've never gotten any weird sensations from the flex and it seems to ride and handle quite well. On-road I liked it less, but much stiffer digressive shocks were a huge improvement everywhere, IMO.
Regarding "suspension tuning"... Back then I don't think any manufacturers used more than 2 brain cells working 5 minutes to design the suspensions on trucks. Leaf springs to carry whatever load you want to design it for and slap a cheap shock on it. If someone wants use it to haul bigger loads, or actually perform offroad, they'll upgrade it anyway. Keeps the aftermarket in business!