For clarity of discussion, I'm going to use the City Connection covers as a point of reference (chosen arbitrarily because I provided the scans

)
The cover listed as Retail is what the actual retail box looks like.
The first cover listed as Custom is mostly the same, but has the logo on the spine flipped around to match the direction that the English language is normally written on spines of books, boxes, covers, etc. (seriously, Jaleco, get it together!)
The second cover listed as Custom is modified to match the "standard" layout for NES game covers that most have adopted. The front and back still match the retail cover, but the spine is modified to have the black box with the Nintendo Entertainment System logo on the top, the publisher's logo on the bottom, and the game's logo somewhere in the middle (in this case, lower than it is on the Retail cover, and facing the proper direction as in the other Custom cover)
I think what I'm calling a template are the covers we see when we click retail on the NES section. Most have the logo at the top of the spine
Any covers that have the black box with the "Nintendo Entertainment System" logo on the top of the spine and are listed as Retail are mislabeled. Those
should be listed as Custom.