Are you asking about FAA or ASTM (LSA) certified engines?
My understanding is that for ASTM, a manufacturer may set the TBO to the longest time that a copy of that engine model has run properly without changing any parts.
Otherwise I think the TBO may also be determined from shorter runs by measuring the wear of parts and interpolating when the fastest wearing part will reach the acceptable size limit set by the designers.
But I can't swear to any of the above; it is just my understanding. That so many engines have nice round numbers near multiples of a thousand hours rather suggests there is a lot of conservative interpolation going on.
