In 1960s or earlier, an organist could pick one playing and learning style and apply it to all of his or her repertoire. For example, the legendary organ methods by Dupre, Gleason, and many others all taught the legato style in organ performance.
So in those days, if you wanted to play organ works of Buxtehude, Bach, Couperin, Liszt, or Franck, you would be playing everything legato (with some notable exceptions, of course). The legato school of organ playing would be very systematic and organists could produce great results.
However, this approach is no longer working because there is so much information available concerning performance practice. Since the repertoire of organ music is so vast in variety (national styles, historical periods etc.) I think we have to approach each style and school differently.
Otherwise our playing would be the same regardless if we play music of Frescobaldi, Bach, Buxtehude, Couperin, Mendelssohn, Schlick, Messiaen, Franck, Cabezon or any other composer. Nowadays, the best organ method books teach different organ playing styles differently.
If you are looking for the answer to the question what is the best method in learning organ playing, you should be looking into various organ schools individually and taking what is best in each approach for the given piece.
In other words, if you are studying works by Frescobaldi, try to find some information about the performance practice of the Italian Baroque or North German Baroque for the music of Buxtehude.
The different national and historical schools had their own view on such performance practice issues, as articulation, fingering, pedaling, registration, ornamentation etc.
The composers influenced organ builders to build specific instruments for particular region and time. Likewise, organ builders wanted to include some innovations or certain features in their organs and composers adjusted their music to the changes as well.
Note that the legato school is still very much valid for the Romantic and Modern organ music. However, even here you have so much variety and options in the different national styles (German, French, English etc.)
Use the above tips when you are studying the works of different composers of various historical periods and national schools. Do not play them in one style but try to recreate all performance practice details to help your playing sound more authentic.
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