Lots of professional MIDI instruments provide for alternative temperaments, which is part of the MIDI 1.0 specification. It's not hard to render things in just intonation.
Instruments like the lyre (second video) are most easily tuned to themselves, so I see no basis for the presumption about that either.
> Lots of professional MIDI instruments provide for alternative temperaments
How about the cheap and nasty MIDI instrument this recording was made with?
I actually really love the fact that this ancient tune, which by virtue of its age is one of humanity's most precious cultural possessions (worth three Great Pyramids, two complete works of Shakespeare, or about thirty Mona Lisas, i'd say), is here reproduced with all the cheesy gusto that Bad MIDI can muster. It's like printing the Odyssey on toilet paper. In comic sans.
You can use a tuning fork, but that doesn't matter. Temperament is about the tuning relationships between notes of the scale. In equal temperament they're slightly enharmonic, ie adjusted away from ideal harmony in order to allow transposition into different keys. This doesn't sound as pretty, but it's 'equally bad' across all keys and we're used to it. If you tune strings against each other then the intervals are consonant. Your starting pitch can be rather arbitrary as long as you're not trying to match it to any other instrument. If you are trying to match to another instrument (in ancient times, a horn was the most likely candidate) then you blow a note on that and tune one string to it.
Musical key intervals are based on simple mathematical ratios, which haven't changed in the interim.
Instruments like the lyre (second video) are most easily tuned to themselves, so I see no basis for the presumption about that either.