It really boils down to the number made in the limited edition. The R&D costs need to be spread over thousands of units in order for the watch to be profitable, if you're spreading it over a few hundred, then in order for it to be profitable, it's going to be very expensive.
Some companies simply don't make a profit on some watches, but they're exhibits of technological know-how.
Let's take Formula 1 racing. This is a most unprofitable endeavor. But they do it simply to prove the car company has the technical know-how to make it.
Many times, these companies store a limited edition away and then make a new movement but adding upon the base movement of that LE. Take the Jaeger-LeCoultre Reverso Septieme; this movement is basically a Reverso Grande Date with a day/night indicator. Whoa, look at the Reverso Grande GMT. The Septieme is basically a Grande GMT without the second time zone.
The Septieme would be one of those pseudo limited editions.