So the long of the short of it, my guitar tech and I were trying to figure out the best way to go about doing these, since my guitar had tabs routed out from the previous owner we had a little bit of extra slack to play with.
What the tech ended up doing was filing down the pickup tabs a bit, and screwing the EMG's into the the new rerouted pickup tabs.
This holds the pickup in place, and allows you to adjust the height or even replace the pick up in the future if you want.
There is no tonal difference with the cover on or off, and i think it makes the guitar look a lot more uniform.
The pick ups currently in the guitar
Bridge: EVO 7
Neck: Air Norton 7
Here is how it looks
So, you guys made pickup covers and just stuck the pickups inside of them? The way you described it, i'm not sure exactly what you're talking about here.