From Web Search of the Periodic Table ....
"Plutonium-239 is one of the three fissile materials used for the production of nuclear weapons and in some nuclear reactors as a source of energy. The other fissile materials are uranium-235 and uranium-233. Plutonium-239 is virtually non-existent in nature. It is made by bombarding uranium-238 with neutrons in a nuclear reactor. Uranium-238 is present in quantity in most reactor fuel; hence plutonium-239 is continuously made in these reactors. Since plutonium-239 can itself be split by neutrons to release energy, plutonium-239 provides a portion of the energy generation in a nuclear reactor."

Fissile material left over from an exploded nuclear device creates quite the mess ...and its contamination and very small particles that are very radioactive that can cause the most damage to humans. You don't have to be able to "see it" for it to hurt you.

Any shelter designed as bomb shelter should be adequate to handle a tornado. Though all the designs I ever looked at were below ground. That said ...and as stated before...with adequate funds ...you could build an above ground structure from re-inforced concrete and steel that would weather a tornado ...but again ... it would or coudn't have windows unless they were able to be sealed with something akin to blast doors or seriously strong shutters. Which could be done ...but again ... bring your checkbook.
I've seen storm shelters incorporated into home designs that are marketed as "safe rooms" ...most are re-inforced concrete and/or serious steel that are left standing after hurricanes and tornados tore the house down around it. But most are fairly small like maybe 8 x 8 at most. They won't stand up to a bomb blast but will weather a natural disaster. Though they'd be small. Taking that concept further you could build the basement as if it were a large storm shelter ... have a large space that could survive the storm ....your "basement roof would be the house subfloor...but you'd have to rebuild your house.
To make any "normal" looking house survive it would need to be largely re-inforced concrete with enough "lipstick" on the facade to make it look "normal" ....but its gonna be hard to seal the openings (doors/windows) in a way that doesn't make it look sinister...and it will cost a lot of $$$.
But the bigger it was, the more it would cost ... so clearly something under or around 1000 sq ft, single story, simple design... would be a more cost-effective target goal than your 3000 sq ft yuppie mini-mansion.
NO design could protect you if you weren't in it though ...and sealing yourself up in your habitat every night presents more issues to content with.