When I saw the initial press releases for Laputa & Yamadas I sent a question to the email attached, regarding why these didn't fit into order with the existing Studio Ghibli blu-ray releases, ie Ponyo was #17 and Nausicaä #1 so they should have been Laputa #2 and Yamadas #12.
They were initially numbered 2 & 3, so I thought they had just made a mistake with My Neighbours the Yamadas, so was emailing them to say it should be #12.

Received a reply stating that they had "made a mistake" with both the Ponyo & Nausicaä releases and that they were going to be re-released with numbering reflecting release date ie. Ponyo #1 & Nausicaä #2
Then the press releases were updated and Laputa & Yamadas were numbered 3 & 4

So basically, they could have had numbering that reflected the dates which the Studio Ghilbli films were produced, with little to no effort on there part. But instead of just changing Yamadas (change the numbering, probably well before production at that stage), they decided to re-release the existing titles and make the Ponyo and Nausicaä copies with original numbering "collector’s items", and yes they did actually say that.