Ok, here are some basic rules of thumb,
1. Bridge pickups tend to be hotter, and therefore can sound muddy in the neck most of the time, but NOT ALWAYS.
2. F- spacing is only a big issue on fender style guitars (Ibanez, Jackson, other Floyd Rose equiped guitars) Regular spacing should work well in either position on a Les Paul or similar instruments.
3. Neck Pickups are often weaker and therefore don't do well in the bridge for a high gain sound.
4. A lot of bridge pickups have more emphasis in the low end to compensate for the thin sound create so close to the bridge. Conversely Neck pickups have an emphasis in the higher frequencies to add clarity to the neck position.
5. Typically the bridge is the hottest, followed by the neck, and then the middle is the weakest.
In your situation, they very well could be the same pickup. Nothing is wrong with that. Steve Vai used the Paf Pro in the neck and bridge of many of his Jem guitars. The only difference is the spacing because of the tremolos tendency to flare out the strings.
For the record, I have a non-f-spaced Dimarzio evolution in the bridge of an Ibanez Rg. The polepieces don't line up cosmeticaly, but everything sounds ok to my deaf ears.