HI Stephen,
The centreline setting is correct. This setting is to compensate for the thickness of the holder and the angle at which the flange is fitted.
Your habit of dipping is also fine. Dipping just enough to cover the eyelet is fine.
Getting ink on the flange is not really a problem as Brass is quite resistant to corrosion. Just have to wash it out with water if you get ink on it, as you don't want the ink to dry up in the gap where you insert the nib.
With regard to the wrong oblique. Is this the Colonial oblique starter kit? I have not used this holder, but I am presuming that if PIA is selling this with a Nikko, it should to suitable for one. However, each person's grip, size of hand, placement of fingers on the holder varies. Ideally oblique holders with a brass flange should be adjusted to your particular grip and nib.
As Gary said you can start loading the nib with a dropper or a brush if you are worried about the flange getting ink. But if you find that too cumbersome you could try the following.
Two things you can look at to see if it helps.
One is the inward cant of the flange. Chris Yoke had a brilliant video for adjusting angles of the flange
This one is for the angles. The inward cant adjustment is a 4:40 mins
After you adjust the Cant you may find that you need to slide the nib in or out a little more to match the centre line.
Second is adjusting the flange itself
This video is for adjusting the flange to take a new nib.
I hope this helps.
Happy writing
-Prasad