If you tune the intervals between different pairs of notes exactly, then the intervals and notes defined by our standard keyboard don't quite fit together; this is just a sad fact of maths. To make them fit, you have to tune the intervals slightly wrong, which is called "tempering" the intervals, and the pattern of how you temper all the different intervals on the keyboard is called a "temperament". The commonest way of doing this in modern times is simply to space the notes in the octave evenly, known as "equal temperament" - this give fifths that are slightly flat (too narrow), and major thirds that are markedly sharp (too wide), but all by the same amount for a given type of interval.
On instruments like the organ, the effect of the sharp thirds, in particular, is very apparent, because of the evenly held sounds from the pipes. So temperaments are used which make the most commonly used major thirds closer to the correct tuning - but this can only be done by making other thirds worse; hence the idea of good keys and bad keys, according to which thirds they contain. This discussion is usually had referring to fifths; but the thirds are more important because that's where the big errors are. In any case, all the adjustments have to be done at the same time so as to fit together.
If you try to make as many intervals accurate as possible, throwing all the errors onto one interval, this interval is so bad that it is known as "the wolf". Renaissance and early Baroque tunings tried to make the five most important major thirds accurate, and then the rest pretty good, leaving one as the wolf. These tunings were called "mean-tone temperaments". In the later Baroque era, the thirds were compromised enough to make all keys playable, though some were better and some were worse - these are now called "well temperaments" (after Bach's collection of pieces in all keys called "The Well-Tempered Klavier"). In the Victorian period, equal temperament came to the fore; but modern authenticity movements have led to a resurgence of the use of older unequal temperaments.
In the case of an organ, changing the temperament is a major undertaking, which may require many of the pipes to be rebuilt in the workshop. So once a temperament has been chosen for an organ, it is not changed except possibly as part of a major rebuild. A harpsichord player, on the other hand, will tune his instrument for every concert, and can choose to use a different temperament each time (though not many would bother to keep changing).
As for pipe-organ builders... Their industry is in steep decline, perhaps more obviously in the UK than anywhere else, and any hint that a cheaper alternative might be acceptable in place of a real organ is taken very hard. It is difficult to find the balance between preserving the centuries-old craft and turning to something more affordable; but it is clear that electronic substitutes, even the sophisticated ones I am using, are still a long way from being able to truly replace the real thing.