A maxillary denture needs a seal to be retentive. The denture borders have to end on, and remain in contact with, soft tissue for a seal to be maintained.
There are two main problems that are solved by using a seal.
(1) Processing causes a distortion across the posterior border of the maxillary denture. The palatal seal helps to compensate for this inaccuracy.
(2) Except for the posterior border, the muco-buccal fold (soft tissue) will move with the denture and maintain the seal. The soft palate moves independently of the denture thus there is a need to modify the posterior border of the denture to keep a seal.
There is a portion of the soft palate that does not move because it is attached to the bony palate. Here the bony palate and soft palate overlap. This is the area of the posterior palatal seal. Your complete denture will end on soft tissue which overlies the palatine bone.
Every portion of your maxillary denture is supported by bone, including the soft palate area. If the palatal seal is made too deep then it will act like a shim rather than a seal and actually prevent the denture from seating.