I truly understand your point of view. To prove I understand it, here is a pic of my own Jagmaster...

I did exactly what you plan to do: modded it to make it better suited to me. I left the stock JagMast pickup in the neck position. I didn't like the one in the bridge, so it went.
When I posted the last reply, I really didnt feel like talking guitars, so I just posted a very base opinion on the matter. I'm usually not that gruff.
As you can already tell, the Jagmaster is a great guitar, but in choosing replacement pickups, proceed carefully.
Remember that the guitar has a swimming pool rout, and no shielding on the pickguard. The wrong pickups might feed back more than desired.
As for the difference between 'Seymour Duncan', and 'Duncan Designed', it's much the same as the difference between Fender and Squier. The DD's are made in Korea using cheaper labour, cheaper components, and looser quality control. Outside of that, they are made more or less to emulate the SD HB101.
The worst thing about buying aftermarket pickups - and the reason I have not spent more when I have done it - is because it's so hard to try before you buy.
I would suggest typing the names of some pickups you are considering into youtube and taking a looksee. The people who post those vids are usually willing to answer questions too.