I know what you are talking about. I guess I just lucked out on this particular setup and it works.
But as you said. There is often an issue with some spacing. Way back... around 30 years ago...
I had a 5 string custom built. Playing left handed, a leftie 5 string DID NOT exist. This was about the time when 5 strings were just starting out. I went to a shop in Toronto, Ontario Canada called the 12th Fret. I had them build me a custom 5 string left handed. I was so lucky to get a luthier named Gordon Barry that was working there at the time. He was given the job of building my bass. It turned out awesome!! Gordon Barry is the man

(
http://www.gwbarryguitars.com/1About/indexAbout.html )
At the time, there were no 5 string bass pickups. And I mean none, Aftermerket... Some manufacturers had some available to them or had their own made. I didn't have that luxury. I had to use an EMG P-Jazz active 4 string set. Much like Mike Inez put in his "Moon Bass". They sounded great. But the P bass pick up wasn't designed for a 5 string set up. I had a luthier in Ottawa Canada do new set up, fret dress, etc after a number of years of abuse.
He told me that the spacing was doing weird things. The "A" string was sitting "FAT and HAPPY!!" right in the middle. I never forgot that LOL