Do you know if the 1HDT is in that list?
It's not. Since the 1HD-t was never sold by Toyota in the US, it is not EPA certified.
In order to qualify for the EPA exemption, the motor in the car needs to be
either: the original (or original type) motor that was in the car when it was manufactured;
or an EPA certified motor (i.e. a motor originally sold in the USA). In either case, all original emissions equipment must be present.
It can be discussed that a 1HDT is one of the “options” for the model, in that country. In fact, it is the original engines used. Therefore, if the vehicle is imported as a 25 year old vehicle, not as a “re-import of a USDM vehicle back into the US”, would we be fine?
Well...I didn't notice where "that country" is, and maybe the 80 series was offered with a 1HD-t there, but ultimately it doesn't matter. If you import the car as being 25+ years old, you will need to file an EPA 3520 with US Customs declaring that the car is in "original unmodified condition", which isn't really true in this case.
I understand that there’s some risk involved.
The risk is in declaring things to Customs that aren't actually true. You may get caught, or you may not. If it slides through Customs, then yay! for you. OTOH, if Customs determines that you aren't allowed to bring the car into the US, you'll have the option to ship it somewhere that will have it--either where you started or a third country. If you opt not to ship it out of the US, it will likely be confiscated and may be destroyed.
what’s the difference between and 6BT-engine swapped FZJ80 here in the US
6BT is EPA certified. It was sold as original equipment in vehicles here in the US.
Your other option is to treat it as a re-importation of a vehicle originally sold in the US, but that comes with it's own set of problems. Per the CBP website:
"Re-Importing A Previously Exported Vehicle - A vehicle taken from the United States for non-commercial, private use may be returned duty free by proving to CBP that it was previously owned and registered in the United States. This proof may be a state-issued registration card for the automobile or a bill of sale for the car from a U.S. dealer. Repairs or accessories acquired abroad for your vehicle must be declared on your return and may be subject to duty."
Which means that you'd need to declare the motor swap (and possibly pay duty on its value). Once you declare the motor swap, you may have some awkward questions to answer about the engine's status with the EPA. Or not.
It all boils down to your tolerance of risk, and maybe having a plan B ready in case things go south. I've heard accounts of modified cars (motor swaps and/or modified or deleted emissions equipment) getting through US Customs without incident. How much do you love the car? And, do you feel lucky?