It was actually the lobster fishery in the Maritimes region. In lobster fishing areas 33 and 34 on the southwest coast of Nova Scotia, they have been limited since 1980 to vessels that are no more than 45 feet in length overall. In the late 1990s and early 2000s, people were pushing and at times surpassing that limit, and found that they were able to get away with it by the stern extensions, which weren't being registered in DFO's licensing system as part of the length overall of the vessel.
In 2002, following a couple of years of consultation with the advisory committees of those two groups, the department did mail out a ballot, a survey, to license-holders in those areas, asking if they wanted the 44'11'' limit to be respected, if there was any leeway for a stern extension, and what such a stern extension should look like. There was majority support to maintain the limit at 45 feet, but there was also majority support to allow a moderate extension of no more than five feet.
To get back to the beginning of your question about the motivations, I could make a supposition but it would be just that. I expect it would be to carry more gear so they can do it in one trip instead of two trips, and to be able to haul more fish.